sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | gmap 2024-11-20+ds-2 (amd64) Mon, 30 Jun 2025 14:30:30 +0000 | +==============================================================================+ Package: gmap Version: 2024-11-20+ds-2 Source Version: 2024-11-20+ds-2 Distribution: perl-5.40-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Mon, 30 Jun 2025 14:30:31 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gmap_2024-11-20+ds-2 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup gmap_2024-11-20+ds-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Mon, 30 Jun 2025 14:30:31 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.40 InRelease [3042 B] Hit:3 http://localhost:3142/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Mon, 30 Jun 2025 14:30:37 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/gmap_2024-11-20+ds-2.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Mon, 30 Jun 2025 14:30:37 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev, build-essential Filtered Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev, build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ InRelease Get:2 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ Release [609 B] Ign:3 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ Release.gpg Get:4 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ Sources [690 B] Get:5 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ Packages [729 B] Fetched 2028 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl liblocale-gettext-perl libmagic-mgc libmagic1t64 libpipeline1 libsimde-dev libtool libuchardet0 libxml2 m4 man-db po-debconf sensible-utils zlib1g-dev Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx bzip2-doc libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: architecture-properties autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libbz2-dev libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl liblocale-gettext-perl libmagic-mgc libmagic1t64 libpipeline1 libsimde-dev libtool libuchardet0 libxml2 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils zlib1g-dev 0 upgraded, 35 newly installed, 0 to remove and 0 not upgraded. Need to get 12.4 MB/12.4 MB of archives. After this operation, 51.2 MB of additional disk space will be used. Get:1 file:/srv/reprepro perl-5.40/main amd64 liblocale-gettext-perl amd64 1.07-7+b2 [15.3 kB] Get:2 copy:/build/gmap-Yvd6ZU/resolver-aMrWxm/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B] Get:3 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.25 [25.0 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2 [243 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41-5 [94.6 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 architecture-properties amd64 0.2.6 [2336 B] Get:14 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-8 [294 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.24.2 [90.9 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-4 [539 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:23 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get:25 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-1 [698 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2 [1680 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:30 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:31 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.24.2 [919 kB] Get:32 http://deb.debian.org/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:33 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get:34 http://deb.debian.org/debian unstable/main amd64 libsimde-dev all 0.8.2-3 [467 kB] Get:35 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Preconfiguring packages ... Fetched 12.4 MB in 0s (97.7 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 23092 files and directories currently installed.) Preparing to unpack .../00-liblocale-gettext-perl_1.07-7+b2_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b2) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.25_all.deb ... Unpacking sensible-utils (0.0.25) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../03-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../04-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. 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Setting up bsdextrautils (2.41-5) ... Setting up libmagic-mgc (1:5.46-5) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up architecture-properties:amd64 (0.2.6) ... Setting up libdebhelper-perl (13.24.2) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2) ... Setting up m4 (1.4.19-8) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up autotools-dev (20240727.1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.25) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-1) ... Setting up liblocale-gettext-perl (1.07-7+b2) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-2) ... Setting up libtool (2.5.4-4) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.24.2) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-9) ... +------------------------------------------------------------------------------+ | Check architectures Mon, 30 Jun 2025 14:30:42 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Mon, 30 Jun 2025 14:30:42 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.44-3 dpkg-dev_1.22.20 g++-13_13.4.0-1 g++-14_14.2.0-19 gcc-13_13.4.0-1 gcc-14_14.2.0-19 libc6-dev_2.41-9 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 linux-libc-dev_6.12.33-1 Package versions: adduser_3.152 apt_3.0.3 architecture-properties_0.2.6 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_13.8 base-passwd_3.6.7 bash_5.2.37-2+b3 binutils_2.44-3 binutils-common_2.44-3 binutils-x86-64-linux-gnu_2.44-3 bsdextrautils_2.41-5 bsdutils_1:2.41-5 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:14.2.0-1 cpp-13_13.4.0-1 cpp-13-x86-64-linux-gnu_13.4.0-1 cpp-14_14.2.0-19 cpp-14-x86-64-linux-gnu_14.2.0-19 cpp-x86-64-linux-gnu_4:14.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.24.2 debian-archive-keyring_2025.1 debianutils_5.23.1 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-2 diffutils_1:3.10-4 dirmngr_2.4.7-21+b1 dpkg_1.22.20 dpkg-dev_1.22.20 dwz_0.15-1+b1 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:14.2.0-1 g++-13_13.4.0-1 g++-13-x86-64-linux-gnu_13.4.0-1 g++-14_14.2.0-19 g++-14-x86-64-linux-gnu_14.2.0-19 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-13_13.4.0-1 gcc-13-base_13.4.0-1 gcc-13-x86-64-linux-gnu_13.4.0-1 gcc-14_14.2.0-19 gcc-14-base_14.2.0-19 gcc-14-x86-64-linux-gnu_14.2.0-19 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-2 gettext-base_0.23.1-2 gnupg_2.4.7-21 gnupg-l10n_2.4.7-21 gnupg-utils_2.4.7-21+b1 gpg_2.4.7-21+b1 gpg-agent_2.4.7-21+b1 gpg-wks-client_2.4.7-21+b1 gpgconf_2.4.7-21+b1 gpgsm_2.4.7-21+b1 gpgv_2.4.7-21+b1 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.25 libapt-pkg7.0_3.0.3 libarchive-zip-perl_1.68-1 libasan8_14.2.0-19 libassuan0_2.5.6-1+b1 libassuan9_3.0.2-2 libatomic1_14.2.0-19 libattr1_1:2.5.2-3 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b2 libbinutils_2.44-3 libblkid1_2.41-5 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libbz2-dev_1.0.8-6 libc-bin_2.41-9 libc-dev-bin_2.41-9 libc-l10n_2.41-9 libc6_2.41-9 libc6-dev_2.41-9 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-9 libcc1-0_14.2.0-19 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-3 libctf0_2.44-3 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.279 libdebhelper-perl_13.24.2 libdpkg-perl_1.22.20 libeatmydata1_131-2+b1 libelf1t64_0.192-4 libffi8_3.4.8-2 libfile-stripnondeterminism-perl_1.14.1-2 libgcc-13-dev_13.4.0-1 libgcc-14-dev_14.2.0-19 libgcc-s1_14.2.0-19 libgcrypt20_1.11.0-7 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgnutls30t64_3.8.9-2 libgomp1_14.2.0-19 libgpg-error0_1.51-4 libgprofng0_2.44-3 libhogweed6t64_3.10.1-1 libhwasan0_14.2.0-19 libidn2-0_2.3.8-2 libisl23_0.27-1 libitm1_14.2.0-19 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41-5 libldap-2.5-0_2.5.19+dfsg-1 libldap2_2.6.10+dfsg-1+b1 liblocale-gettext-perl_1.07-7+b2 liblsan0_14.2.0-19 liblz4-1_1.10.0-4 liblzma5_5.8.1-1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41-5 libmpc3_1.3.1-1+b3 libmpfr6_4.2.2-1 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnpth0t64_1.8-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.45-1 libperl5.38t64_5.38.2-5 libperl5.40_5.40.1-4 libpipeline1_1.5.8-1 libquadmath0_14.2.0-19 libreadline8t64_8.2-6 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe1_2.44-3 libsimde-dev_0.8.2-3 libsmartcols1_2.41-5 libsqlite3-0_3.46.1-6 libssl3t64_3.5.0-2 libstdc++-13-dev_13.4.0-1 libstdc++-14-dev_14.2.0-19 libstdc++6_14.2.0-19 libsystemd0_257.7-1 libtasn1-6_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-4 libtsan2_14.2.0-19 libubsan1_14.2.0-19 libuchardet0_0.0.8-1+b2 libudev1_257.7-1 libunistring5_1.3-2 libuuid1_2.41-5 libxml2_2.12.7+dfsg+really2.9.14-1 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1 linux-libc-dev_6.12.33-1 locales-all_2.41-9 login_1:4.16.0-2+really2.41-5 login.defs_1:4.17.4-2 m4_1.4.19-8 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.0-2 passwd_1:4.17.4-2 patch_2.8-2 perl_5.40.1-4 perl-base_5.40.1-4 perl-modules-5.38_5.38.2-5 perl-modules-5.40_5.40.1-4 pinentry-curses_1.3.1-2 po-debconf_1.0.21+nmu1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.25 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 usr-is-merged_39+nmu2 util-linux_2.41-5 xz-utils_5.8.1-1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 zlib1g-dev_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Mon, 30 Jun 2025 14:30:42 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: gmap Binary: gmap Architecture: any Version: 2024-11-20+ds-2 Maintainer: Debian Med Packaging Team Uploaders: Shaun Jackman , Andreas Tille , Alexandre Mestiashvili , Étienne Mollier Homepage: http://research-pub.gene.com/gmap Standards-Version: 4.7.1 Vcs-Browser: https://salsa.debian.org/med-team/gmap Vcs-Git: https://salsa.debian.org/med-team/gmap.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), architecture-is-little-endian, help2man, libbz2-dev, zlib1g-dev, debhelper, libsimde-dev Package-List: gmap deb science optional arch=any Checksums-Sha1: 62abf6c57d47832f38718b9aaf5187e159257084 2578616 gmap_2024-11-20+ds.orig.tar.xz a946ded506b5dba688b371e3b16faf7539ebcb89 14076 gmap_2024-11-20+ds-2.debian.tar.xz Checksums-Sha256: 82d456442f2249c7c0e3a6bf9cfe3a2cc9b9e434bd9705ac6c0a38f7b01011cd 2578616 gmap_2024-11-20+ds.orig.tar.xz a46f8e7a62e51afe01d27aeb6f56645eb5d90c86864f00a7334eaf308560fee4 14076 gmap_2024-11-20+ds-2.debian.tar.xz Files: e39b9b6d94d52610760153750fcdb512 2578616 gmap_2024-11-20+ds.orig.tar.xz a64a838fc92226d815d91a6cb3a9b86c 14076 gmap_2024-11-20+ds-2.debian.tar.xz Dgit: 6d6d76dbf92b45dc9bd68bd130388cb2de40ec81 debian archive/debian/2024-11-20+ds-2 https://git.dgit.debian.org/gmap -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAme+Ql0UHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdr9bBAAu85nh1jaMUb7FdVvkfUwYWetv/Z/ yn+4097h9PY42IH6w0H0VncSdI1rKa9pMJmq1PnNo15JGaEt5Sg8Mv5kWRFDZr8H UTGhGR1gR0MAlqo/2+VDioCCCR3dpH8vX6A69GVxqGGtgcKYleVVoh/Sy1Pf7amF r1gMf/VPTPR7yrUHKlV4B5aBV3gMCPAp0yo10P9/4IX5Jye9AwiI4gkJTZAqs5mX 9OYse7Lz/OTS6EmK5+F34fhiCY/5O04ro1UmlMlCmJlxEnppTAoRA6Px9NjLmomK wAwq47RmWz40yGTEluH8GH9FGGdkXRgybEgqPUtwQaY6vabQYn+doENjqufn6TzY MQ7UBQtGEQCdMfjq7pFVYyoarAMwGmRXlQO8whsdK2I4B10QNTRuj4WdLLKqmg0I vzRaEWy9NoLMQTgWCLaXZD1RJIM06DFHBaJj25D6uelmZmjTmdQ92OAstVEvLHOd MThtwvYe3isXgxF3V4oFbxKD9Wl7sQxKznSDkmAHkqzbFawN73Xg/FM1TlAGqD+F C6WvqcqhfEOtMsGtDOxuq+XTya51E4zw5dGQe76FP2g+veOzl3VXFxSK+FggPGE7 xBi3rJFTY2HGSkfp6tPCptA6HR0ErncRUrAgEewXp4SwB9llYHQb1fIYri7tXqZC xaH5pwF5yDkMlYw= =kiYB -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./gmap_2024-11-20+ds-2.dsc: no acceptable signature found dpkg-source: info: extracting gmap in /build/gmap-Yvd6ZU/gmap-2024-11-20+ds dpkg-source: info: unpacking gmap_2024-11-20+ds.orig.tar.xz dpkg-source: info: unpacking gmap_2024-11-20+ds-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying install-data-local dpkg-source: info: applying remove_getopt_code_copy.patch dpkg-source: info: applying simd_fixes dpkg-source: info: applying c23.patch Check disk space ---------------- Sufficient free space for build +------------------------------------------------------------------------------+ | Starting Timed Build Commands Mon, 30 Jun 2025 14:30:42 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gmap_2024-11-20+ds-2 perl-5.40-throwaway amd64 --------------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network gmap_2024-11-20+ds-2 perl-5.40-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=en_GB.UTF-8 LANGUAGE=en_GB:en LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds SCHROOT_ALIAS_NAME=perl-5.40-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.40-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.40-amd64-debomatic-c48cb45b-e381-4906-8c26-b352e08cd3ba SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package gmap dpkg-buildpackage: info: source version 2024-11-20+ds-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --builddir build debian/rules override_dh_auto_clean make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_auto_clean --builddir build_avx512 dh_auto_clean --builddir build_avx2 dh_auto_clean --builddir build_sse42 dh_auto_clean --builddir build_sse41 dh_auto_clean --builddir build_ssse3 dh_auto_clean make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_autoreconf_clean -O--builddir=build dh_clean -O--builddir=build dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building gmap using existing ./gmap_2024-11-20+ds.orig.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building gmap in gmap_2024-11-20+ds-2.debian.tar.xz dpkg-source: info: building gmap in gmap_2024-11-20+ds-2.dsc debian/rules binary dh binary --builddir build dh_update_autotools_config -O--builddir=build dh_autoreconf -O--builddir=build configure.ac:104: installing 'config/compile' configure.ac:85: installing 'config/config.guess' configure.ac:85: installing 'config/config.sub' configure.ac:109: installing 'config/install-sh' configure.ac:109: installing 'config/missing' Makefile.am: installing './INSTALL' src/Makefile.am: installing 'config/depcomp' src/Makefile.am:870: warning: variable 'dist_compare2truth_SOURCES' is defined but no program or src/Makefile.am:870: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1216: warning: variable 'dist_gcount_bulk_SOURCES' is defined but no program or src/Makefile.am:1216: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1242: warning: variable 'dist_gcount_sc_SOURCES' is defined but no program or src/Makefile.am:1242: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:216: warning: variable 'dist_gexact_SOURCES' is defined but no program or src/Makefile.am:216: library has 'gexact' as canonical name (possible typo) src/Makefile.am:742: warning: variable 'dist_gexact_arm_SOURCES' is defined but no program or src/Makefile.am:742: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:772: warning: variable 'dist_gexact_avx2_SOURCES' is defined but no program or src/Makefile.am:772: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:778: warning: variable 'dist_gexact_avx512_SOURCES' is defined but no program or src/Makefile.am:778: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:784: warning: variable 'dist_gexact_avx512bw_SOURCES' is defined but no program or src/Makefile.am:784: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:736: warning: variable 'dist_gexact_nosimd_SOURCES' is defined but no program or src/Makefile.am:736: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:748: warning: variable 'dist_gexact_sse2_SOURCES' is defined but no program or src/Makefile.am:748: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:760: warning: variable 'dist_gexact_sse41_SOURCES' is defined but no program or src/Makefile.am:760: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:766: warning: variable 'dist_gexact_sse42_SOURCES' is defined but no program or src/Makefile.am:766: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:754: warning: variable 'dist_gexact_ssse3_SOURCES' is defined but no program or src/Makefile.am:754: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:223: warning: variable 'dist_gfilter_SOURCES' is defined but no program or src/Makefile.am:223: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:816: warning: variable 'dist_gfilter_arm_SOURCES' is defined but no program or src/Makefile.am:816: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:846: warning: variable 'dist_gfilter_avx2_SOURCES' is defined but no program or src/Makefile.am:846: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:852: warning: variable 'dist_gfilter_avx512_SOURCES' is defined but no program or src/Makefile.am:852: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:858: warning: variable 'dist_gfilter_avx512bw_SOURCES' is defined but no program or src/Makefile.am:858: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:810: warning: variable 'dist_gfilter_nosimd_SOURCES' is defined but no program or src/Makefile.am:810: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:822: warning: variable 'dist_gfilter_sse2_SOURCES' is defined but no program or src/Makefile.am:822: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:834: warning: variable 'dist_gfilter_sse41_SOURCES' is defined but no program or src/Makefile.am:834: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:840: warning: variable 'dist_gfilter_sse42_SOURCES' is defined but no program or src/Makefile.am:840: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:828: warning: variable 'dist_gfilter_ssse3_SOURCES' is defined but no program or src/Makefile.am:828: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1132: warning: variable 'dist_iit_pileup_SOURCES' is defined but no program or src/Makefile.am:1132: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1154: warning: variable 'dist_sam_sort_SOURCES' is defined but no program or src/Makefile.am:1154: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1172: warning: variable 'dist_umi_correct_SOURCES' is defined but no program or src/Makefile.am:1172: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1191: warning: variable 'dist_velocity_counts_SOURCES' is defined but no program or src/Makefile.am:1191: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:869: warning: variable 'compare2truth_LDADD' is defined but no program or src/Makefile.am:869: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1215: warning: variable 'gcount_bulk_LDADD' is defined but no program or src/Makefile.am:1215: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1241: warning: variable 'gcount_sc_LDADD' is defined but no program or src/Makefile.am:1241: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:215: warning: variable 'gexact_LDADD' is defined but no program or src/Makefile.am:215: library has 'gexact' as canonical name (possible typo) src/Makefile.am:741: warning: variable 'gexact_arm_LDADD' is defined but no program or src/Makefile.am:741: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:771: warning: variable 'gexact_avx2_LDADD' is defined but no program or src/Makefile.am:771: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:777: warning: variable 'gexact_avx512_LDADD' is defined but no program or src/Makefile.am:777: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:783: warning: variable 'gexact_avx512bw_LDADD' is defined but no program or src/Makefile.am:783: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:735: warning: variable 'gexact_nosimd_LDADD' is defined but no program or src/Makefile.am:735: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:747: warning: variable 'gexact_sse2_LDADD' is defined but no program or src/Makefile.am:747: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:759: warning: variable 'gexact_sse41_LDADD' is defined but no program or src/Makefile.am:759: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:765: warning: variable 'gexact_sse42_LDADD' is defined but no program or src/Makefile.am:765: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:753: warning: variable 'gexact_ssse3_LDADD' is defined but no program or src/Makefile.am:753: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:222: warning: variable 'gfilter_LDADD' is defined but no program or src/Makefile.am:222: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:815: warning: variable 'gfilter_arm_LDADD' is defined but no program or src/Makefile.am:815: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:845: warning: variable 'gfilter_avx2_LDADD' is defined but no program or src/Makefile.am:845: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:851: warning: variable 'gfilter_avx512_LDADD' is defined but no program or src/Makefile.am:851: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:857: warning: variable 'gfilter_avx512bw_LDADD' is defined but no program or src/Makefile.am:857: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:809: warning: variable 'gfilter_nosimd_LDADD' is defined but no program or src/Makefile.am:809: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:821: warning: variable 'gfilter_sse2_LDADD' is defined but no program or src/Makefile.am:821: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:833: warning: variable 'gfilter_sse41_LDADD' is defined but no program or src/Makefile.am:833: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:839: warning: variable 'gfilter_sse42_LDADD' is defined but no program or src/Makefile.am:839: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:827: warning: variable 'gfilter_ssse3_LDADD' is defined but no program or src/Makefile.am:827: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1131: warning: variable 'iit_pileup_LDADD' is defined but no program or src/Makefile.am:1131: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1153: warning: variable 'sam_sort_LDADD' is defined but no program or src/Makefile.am:1153: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1171: warning: variable 'umi_correct_LDADD' is defined but no program or src/Makefile.am:1171: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1190: warning: variable 'velocity_counts_LDADD' is defined but no program or src/Makefile.am:1190: library has 'velocity_counts' as canonical name (possible typo) src/Makefile.am:868: warning: variable 'compare2truth_LDFLAGS' is defined but no program or src/Makefile.am:868: library has 'compare2truth' as canonical name (possible typo) src/Makefile.am:1214: warning: variable 'gcount_bulk_LDFLAGS' is defined but no program or src/Makefile.am:1214: library has 'gcount_bulk' as canonical name (possible typo) src/Makefile.am:1240: warning: variable 'gcount_sc_LDFLAGS' is defined but no program or src/Makefile.am:1240: library has 'gcount_sc' as canonical name (possible typo) src/Makefile.am:214: warning: variable 'gexact_LDFLAGS' is defined but no program or src/Makefile.am:214: library has 'gexact' as canonical name (possible typo) src/Makefile.am:740: warning: variable 'gexact_arm_LDFLAGS' is defined but no program or src/Makefile.am:740: library has 'gexact_arm' as canonical name (possible typo) src/Makefile.am:770: warning: variable 'gexact_avx2_LDFLAGS' is defined but no program or src/Makefile.am:770: library has 'gexact_avx2' as canonical name (possible typo) src/Makefile.am:776: warning: variable 'gexact_avx512_LDFLAGS' is defined but no program or src/Makefile.am:776: library has 'gexact_avx512' as canonical name (possible typo) src/Makefile.am:782: warning: variable 'gexact_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:782: library has 'gexact_avx512bw' as canonical name (possible typo) src/Makefile.am:734: warning: variable 'gexact_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:734: library has 'gexact_nosimd' as canonical name (possible typo) src/Makefile.am:746: warning: variable 'gexact_sse2_LDFLAGS' is defined but no program or src/Makefile.am:746: library has 'gexact_sse2' as canonical name (possible typo) src/Makefile.am:758: warning: variable 'gexact_sse41_LDFLAGS' is defined but no program or src/Makefile.am:758: library has 'gexact_sse41' as canonical name (possible typo) src/Makefile.am:764: warning: variable 'gexact_sse42_LDFLAGS' is defined but no program or src/Makefile.am:764: library has 'gexact_sse42' as canonical name (possible typo) src/Makefile.am:752: warning: variable 'gexact_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:752: library has 'gexact_ssse3' as canonical name (possible typo) src/Makefile.am:221: warning: variable 'gfilter_LDFLAGS' is defined but no program or src/Makefile.am:221: library has 'gfilter' as canonical name (possible typo) src/Makefile.am:814: warning: variable 'gfilter_arm_LDFLAGS' is defined but no program or src/Makefile.am:814: library has 'gfilter_arm' as canonical name (possible typo) src/Makefile.am:844: warning: variable 'gfilter_avx2_LDFLAGS' is defined but no program or src/Makefile.am:844: library has 'gfilter_avx2' as canonical name (possible typo) src/Makefile.am:850: warning: variable 'gfilter_avx512_LDFLAGS' is defined but no program or src/Makefile.am:850: library has 'gfilter_avx512' as canonical name (possible typo) src/Makefile.am:856: warning: variable 'gfilter_avx512bw_LDFLAGS' is defined but no program or src/Makefile.am:856: library has 'gfilter_avx512bw' as canonical name (possible typo) src/Makefile.am:808: warning: variable 'gfilter_nosimd_LDFLAGS' is defined but no program or src/Makefile.am:808: library has 'gfilter_nosimd' as canonical name (possible typo) src/Makefile.am:820: warning: variable 'gfilter_sse2_LDFLAGS' is defined but no program or src/Makefile.am:820: library has 'gfilter_sse2' as canonical name (possible typo) src/Makefile.am:832: warning: variable 'gfilter_sse41_LDFLAGS' is defined but no program or src/Makefile.am:832: library has 'gfilter_sse41' as canonical name (possible typo) src/Makefile.am:838: warning: variable 'gfilter_sse42_LDFLAGS' is defined but no program or src/Makefile.am:838: library has 'gfilter_sse42' as canonical name (possible typo) src/Makefile.am:826: warning: variable 'gfilter_ssse3_LDFLAGS' is defined but no program or src/Makefile.am:826: library has 'gfilter_ssse3' as canonical name (possible typo) src/Makefile.am:1130: warning: variable 'iit_pileup_LDFLAGS' is defined but no program or src/Makefile.am:1130: library has 'iit_pileup' as canonical name (possible typo) src/Makefile.am:1152: warning: variable 'sam_sort_LDFLAGS' is defined but no program or src/Makefile.am:1152: library has 'sam_sort' as canonical name (possible typo) src/Makefile.am:1170: warning: variable 'umi_correct_LDFLAGS' is defined but no program or src/Makefile.am:1170: library has 'umi_correct' as canonical name (possible typo) src/Makefile.am:1189: warning: variable 'velocity_counts_LDFLAGS' is defined but no program or src/Makefile.am:1189: library has 'velocity_counts' as canonical name (possible typo) parallel-tests: installing 'config/test-driver' debian/rules override_dh_auto_configure make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' rm -Rf src/simde DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 cd build && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse2 checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse2 checking SSE2 compiler flags to be used... -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI" dh_auto_configure --reload-all-buildenv-variables --builddir build_ssse3 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes cd build_ssse3 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=ssse3 ax_cv_cpu_has_ssse3_ext=yes ax_cv_compile_ssse3_ext=yes ax_cv_link_tmmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... ssse3 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... ssse3 checking SSSE3 compiler flags to be used... -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 DEB_CFLAGS_MAINT_APPEND="-O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_STTNI" dh_auto_configure --builddir build_sse41 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes cd build_sse41 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse41 ax_cv_cpu_has_sse41_ext=yes ax_cv_compile_sse41_ext=yes ax_cv_link_smmintrin_h=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse41 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse41 checking SSE4.1 compiler flags to be used... -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 dh_auto_configure --builddir build_sse42 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes cd build_sse42 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=sse42 ax_cv_cpu_has_sse42_ext=yes ax_cv_compile_sse42_ext=yes ax_cv_link_nmmintrin_h=yes ax_cv_cpu_has_popcnt_ext=yes ax_make_sse42=yes ax_cv_cpu_has_bmi1_ext=yes ax_cv_compile_bmi_ext=yes ax_cv_link_bmi=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm... yes checking for abm linker support... yes checking for _popcnt32 run support... yes checking for _lzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi... yes checking for bmi linker support... yes checking for _tzcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mavx2... yes checking for immintrin.h header file... yes checking for user-selected SIMD level... sse42 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... sse42 checking SSE4.2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 dh_auto_configure --builddir build_avx2 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes cd build_avx2 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx2 ax_make_avx2=yes ax_cv_cpu_has_bmi2_ext=yes ax_cv_compile_bmi2_ext=yes ax_cv_link_bmi2=yes checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2... yes checking for bmi2 linker support... yes checking for _pext run support... yes checking for user-selected SIMD level... avx2 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx2 checking AVX2 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 dh_auto_configure --builddir build_avx512 -- --with-gmapdb=/var/cache/gmap \ --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no cd build_avx512 && ../configure --build=x86_64-linux-gnu --prefix=/usr --includedir=\${prefix}/include --mandir=\${prefix}/share/man --infodir=\${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --disable-option-checking --disable-silent-rules --libdir=\${prefix}/lib/x86_64-linux-gnu --runstatedir=/run --disable-maintainer-mode --disable-dependency-tracking --with-gmapdb=/var/cache/gmap --bindir=/usr/lib/gmap --enable-simd --with-simd-level=avx512 ax_cv_cpu_has_avx512_ext=yes ax_cv_compile_avx512_ext=yes ax_cv_compile_avx512bw_ext=no ax_cv_link_avx512bw=no checking package version... 2024-11-20 checking CFLAGS... -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking target system type... x86_64-pc-linux-gnu checking for non-Intel CPU... no checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether gcc accepts -g... yes checking for gcc option to enable C11 features... none needed checking whether gcc understands -c and -o together... yes checking for -Wdate-time -D_FORTIFY_SOURCE=2 option for large files... none needed checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... /usr/bin/mkdir -p checking for gawk... no checking for mawk... mawk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking xargs -n works... yes checking dependency style of gcc... none checking whether to enable maintainer-specific portions of Makefiles... no checking bindir... /usr/lib/gmap checking for a working version of perl... /usr/bin/perl checking for gcc... (cached) gcc checking whether the compiler supports GNU C... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to enable C11 features... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking for C compiler vendor... gnu checking for rint in -lm... yes checking for pthreads feature... not specified so enabled by default checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for cc_r... gcc checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for fcntl.h... yes checking for limits.h... yes checking for stddef.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/types.h... (cached) yes checking for inline... inline checking whether byte ordering is bigendian... no checking for an ANSI C-conforming const... yes checking for working volatile... yes checking for size_t... yes checking for off_t... yes checking for caddr_t... yes checking size of unsigned long... 8 checking size of unsigned long long... 8 checking size of off_t... 8 checking for declarations of fseeko and ftello... yes checking whether alloca is enabled... not specified so disabled by default checking whether mmap is enabled... not specified so enabled by default checking for working mmap with MAP_FIXED... yes checking for working mmap with MAP_VARIABLE... no checking for MAP_FILE in mmap... yes checking for MAP_VARIABLE in mmap... no checking for MAP_SHARED in mmap... yes checking for MAP_PRIVATE in mmap... yes checking for MAP_FAILED in mmap... yes checking for MADV_DONTNEED in madvise... yes checking for MADV_WILLNEED in madvise... yes checking for MADV_RANDOM in madvise... yes checking for MADV_SEQUENTIAL in madvise... yes checking for SHM_NORESERVE in shmget... yes checking for ceil... yes checking for floor... yes checking for index... yes checking for log... yes checking for madvise... yes checking for memcpy... yes checking for memmove... yes checking for memset... yes checking for munmap... yes checking for pow... yes checking for rint... yes checking for stat64... yes checking for strtoul... yes checking for sysconf... yes checking for sysctl... no checking for sigaction... yes checking for shmget... yes checking for shmctl... yes checking for shmat... yes checking for shmdt... yes checking for semget... yes checking for semctl... yes checking for semop... yes checking for struct stat64... no checking for pagesize via sysconf... yes checking for pagesize via sysctl... no checking whether fopen accepts "b" mode... yes checking whether fopen accepts "t" mode... yes checking for gcc options needed to detect all undeclared functions... none needed checking whether C compiler accepts -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -mpopcnt... yes checking whether __builtin_popcount is declared... yes checking whether __builtin_popcount works... yes checking whether __builtin_clz is declared... yes checking whether __builtin_clz works... yes checking whether __builtin_ctz is declared... yes checking whether __builtin_ctz works... yes checking whether __builtin_clzll is declared... yes checking whether __builtin_clzll works... yes checking whether __builtin_ctzll is declared... yes checking whether __builtin_ctzll works... yes checking for bsr instruction in assembly... no checking if compiler requires an immediate in sse2 _mm_slli_epi32 command... no checking if compiler has STTNI commands... yes checking for _mm_extract_epi64... yes checking for _mm_popcnt_u64... yes checking for whether simd is enabled... enabled checking for sse2 support... yes checking for ssse3 support... yes checking for sse4.1 support... yes checking for sse4.2 support... yes checking for popcnt support... yes checking for bmi1 support... no checking for avx2 support... yes checking for bmi2 support... no checking for avx512 support... no checking for avx512bw and avx512vl support... no checking whether C compiler accepts -msse2... yes checking for emmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3... yes checking for tmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1... yes checking for smmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2... yes checking for nmmintrin.h header file... yes checking for mm_popcnt run support... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2... yes checking for immintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd... yes checking for nmmintrin.h header file... yes checking whether C compiler accepts -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw... yes checking for avx512vl and avx512bw linker support... yes checking for user-selected SIMD level... avx512 checking gmapdb... /var/cache/gmap checking for zlib support... enabled checking for zlib.h... yes checking for gzopen in -lz... yes checking for gzeof in -lz... yes checking for gzgetc in -lz... yes checking for gzgets in -lz... yes checking for gzclose in -lz... yes checking if zlib package is complete... working checking for gzbuffer in -lz... yes checking for bzlib support... enabled checking for bzlib.h... yes checking for BZ2_bzReadOpen in -lbz2... yes checking for BZ2_bzRead in -lbz2... yes checking for BZ2_bzReadClose in -lbz2... yes checking if bzlib package is complete... working checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating util/Makefile config.status: creating util/gmap_process.pl config.status: creating util/gmap_build.pl config.status: creating util/gmap_cat.pl config.status: creating util/md_coords.pl config.status: creating util/fa_coords.pl config.status: creating util/psl_splicesites.pl config.status: creating util/psl_introns.pl config.status: creating util/psl_genes.pl config.status: creating util/ensembl_genes.pl config.status: creating util/gtf_splicesites.pl config.status: creating util/gtf_transcript_splicesites.pl config.status: creating util/gtf_introns.pl config.status: creating util/gtf_genes.pl config.status: creating util/gff3_splicesites.pl config.status: creating util/gff3_introns.pl config.status: creating util/gff3_genes.pl config.status: creating util/dbsnp_iit.pl config.status: creating util/gvf_iit.pl config.status: creating util/vcf_iit.pl config.status: creating tests/Makefile config.status: creating tests/align.test config.status: creating tests/coords1.test config.status: creating tests/setup1.test config.status: creating tests/iit.test config.status: creating src/config.h config.status: executing depfiles commands checking standard compiler and flags to be used... gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration checking standard linker flags to be used... checking pthread compiler flags to be used... checking popcnt flags to be used... -mpopcnt checking compile level... avx512 checking AVX512 compiler flags to be used... -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw # skipping avx512bw for now: # ../../src/oligoindex_hr.c: In function 'count_positions_fwd_simd': make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' debian/rules override_dh_auto_build make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_auto_build cd build && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-cat.c: In function ‘main’: ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_sse2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_sse2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.sse2 gmap_sse2-except.o gmap_sse2-assert.o gmap_sse2-mem.o gmap_sse2-intlist.o gmap_sse2-uintlist.o gmap_sse2-list.o gmap_sse2-littleendian.o gmap_sse2-bigendian.o gmap_sse2-univinterval.o gmap_sse2-interval.o gmap_sse2-stopwatch.o gmap_sse2-semaphore.o gmap_sse2-access.o gmap_sse2-filestring.o gmap_sse2-iit-read-univ.o gmap_sse2-iit-read.o gmap_sse2-md5.o gmap_sse2-bzip2.o gmap_sse2-fopen.o gmap_sse2-sequence.o gmap_sse2-reader.o gmap_sse2-genomicpos.o gmap_sse2-compress.o gmap_sse2-compress-write.o gmap_sse2-gbuffer.o gmap_sse2-genome.o gmap_sse2-popcount.o gmap_sse2-dinucl_bits.o gmap_sse2-genome_canonical.o gmap_sse2-genome-write.o gmap_sse2-bitpack64-read.o gmap_sse2-bitpack64-readtwo.o gmap_sse2-indexdb.o gmap_sse2-oligo.o gmap_sse2-block.o gmap_sse2-chrom.o gmap_sse2-segmentpos.o gmap_sse2-chrnum.o gmap_sse2-uinttable_rh.o gmap_sse2-gregion.o gmap_sse2-match.o gmap_sse2-matchpool.o gmap_sse2-diagnostic.o gmap_sse2-stage1.o gmap_sse2-diag.o gmap_sse2-diagpool.o gmap_sse2-cmet.o gmap_sse2-atoi.o gmap_sse2-orderstat.o gmap_sse2-oligoindex_hr.o gmap_sse2-intron.o gmap_sse2-maxent.o gmap_sse2-maxent_hr.o gmap_sse2-pair.o gmap_sse2-pairpool.o gmap_sse2-cellpool.o gmap_sse2-stage2.o gmap_sse2-doublelist.o gmap_sse2-smooth.o gmap_sse2-splicestringpool.o gmap_sse2-splicetrie_build.o gmap_sse2-splicetrie.o gmap_sse2-boyer-moore.o gmap_sse2-dynprog.o gmap_sse2-dynprog_simd.o gmap_sse2-dynprog_single.o gmap_sse2-dynprog_genome.o gmap_sse2-dynprog_cdna.o gmap_sse2-dynprog_end.o gmap_sse2-translation.o gmap_sse2-pbinom.o gmap_sse2-changepoint.o gmap_sse2-stage3.o gmap_sse2-request.o gmap_sse2-result.o gmap_sse2-output.o gmap_sse2-inbuffer.o gmap_sse2-samheader.o gmap_sse2-printbuffer.o gmap_sse2-outbuffer.o gmap_sse2-chimera.o gmap_sse2-datadir.o gmap_sse2-parserange.o gmap_sse2-getline.o gmap_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.sse2 gmapl_sse2-except.o gmapl_sse2-assert.o gmapl_sse2-mem.o gmapl_sse2-intlist.o gmapl_sse2-uintlist.o gmapl_sse2-uint8list.o gmapl_sse2-list.o gmapl_sse2-littleendian.o gmapl_sse2-bigendian.o gmapl_sse2-univinterval.o gmapl_sse2-interval.o gmapl_sse2-stopwatch.o gmapl_sse2-semaphore.o gmapl_sse2-access.o gmapl_sse2-filestring.o gmapl_sse2-iit-read-univ.o gmapl_sse2-iit-read.o gmapl_sse2-md5.o gmapl_sse2-bzip2.o gmapl_sse2-fopen.o gmapl_sse2-sequence.o gmapl_sse2-reader.o gmapl_sse2-genomicpos.o gmapl_sse2-compress.o gmapl_sse2-compress-write.o gmapl_sse2-gbuffer.o gmapl_sse2-genome.o gmapl_sse2-popcount.o gmapl_sse2-dinucl_bits.o gmapl_sse2-genome_canonical.o gmapl_sse2-genome-write.o gmapl_sse2-bitpack64-read.o gmapl_sse2-bitpack64-readtwo.o gmapl_sse2-indexdb.o gmapl_sse2-oligo.o gmapl_sse2-block.o gmapl_sse2-chrom.o gmapl_sse2-segmentpos.o gmapl_sse2-chrnum.o gmapl_sse2-uinttable_rh.o gmapl_sse2-uint8table_rh.o gmapl_sse2-gregion.o gmapl_sse2-match.o gmapl_sse2-matchpool.o gmapl_sse2-diagnostic.o gmapl_sse2-stage1.o gmapl_sse2-diag.o gmapl_sse2-diagpool.o gmapl_sse2-cmet.o gmapl_sse2-atoi.o gmapl_sse2-orderstat.o gmapl_sse2-oligoindex_hr.o gmapl_sse2-intron.o gmapl_sse2-maxent.o gmapl_sse2-maxent_hr.o gmapl_sse2-pair.o gmapl_sse2-pairpool.o gmapl_sse2-cellpool.o gmapl_sse2-stage2.o gmapl_sse2-doublelist.o gmapl_sse2-smooth.o gmapl_sse2-splicestringpool.o gmapl_sse2-splicetrie_build.o gmapl_sse2-splicetrie.o gmapl_sse2-boyer-moore.o gmapl_sse2-dynprog.o gmapl_sse2-dynprog_simd.o gmapl_sse2-dynprog_single.o gmapl_sse2-dynprog_genome.o gmapl_sse2-dynprog_cdna.o gmapl_sse2-dynprog_end.o gmapl_sse2-translation.o gmapl_sse2-pbinom.o gmapl_sse2-changepoint.o gmapl_sse2-stage3.o gmapl_sse2-request.o gmapl_sse2-result.o gmapl_sse2-output.o gmapl_sse2-inbuffer.o gmapl_sse2-samheader.o gmapl_sse2-printbuffer.o gmapl_sse2-outbuffer.o gmapl_sse2-chimera.o gmapl_sse2-datadir.o gmapl_sse2-parserange.o gmapl_sse2-getline.o gmapl_sse2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.sse2 gsnap_sse2-except.o gsnap_sse2-assert.o gsnap_sse2-mem.o gsnap_sse2-intlist.o gsnap_sse2-uintlist.o gsnap_sse2-list.o gsnap_sse2-littleendian.o gsnap_sse2-bigendian.o gsnap_sse2-univinterval.o gsnap_sse2-interval.o gsnap_sse2-stopwatch.o gsnap_sse2-semaphore.o gsnap_sse2-access.o gsnap_sse2-filestring.o gsnap_sse2-iit-read-univ.o gsnap_sse2-iit-read.o gsnap_sse2-bzip2.o gsnap_sse2-reader.o gsnap_sse2-genomicpos.o gsnap_sse2-compress.o gsnap_sse2-genome.o gsnap_sse2-transcriptome.o gsnap_sse2-popcount.o gsnap_sse2-genomebits.o gsnap_sse2-genomebits_consec.o gsnap_sse2-genomebits_count.o gsnap_sse2-genomebits_kmer.o gsnap_sse2-genomebits_indel.o gsnap_sse2-genomebits_decode.o gsnap_sse2-genomebits_mismatches.o gsnap_sse2-genomebits_trim.o gsnap_sse2-dinucl_bits.o gsnap_sse2-genome_sites.o gsnap_sse2-bitpack64-read.o gsnap_sse2-bitpack64-readtwo.o gsnap_sse2-mergeinfo.o gsnap_sse2-merge-diagonals-heap-uint4.o gsnap_sse2-merge-uint4.o gsnap_sse2-merge-diagonals-simd-uint4.o gsnap_sse2-indexdb.o gsnap_sse2-localdb-read.o gsnap_sse2-oligo.o gsnap_sse2-chrnum.o gsnap_sse2-maxent_hr.o gsnap_sse2-mapq.o gsnap_sse2-fopen.o gsnap_sse2-shortread.o gsnap_sse2-junction.o gsnap_sse2-concordance.o gsnap_sse2-simplepair.o gsnap_sse2-orderstat.o gsnap_sse2-intlistpool.o gsnap_sse2-uintlistpool.o gsnap_sse2-listpool.o gsnap_sse2-hitlistpool.o gsnap_sse2-pathpool.o gsnap_sse2-auxinfopool.o gsnap_sse2-pathstorepool.o gsnap_sse2-intron.o gsnap_sse2-gbuffer.o gsnap_sse2-select64-common.o gsnap_sse2-select64-ones.o gsnap_sse2-select64-zeroes.o gsnap_sse2-ef64.o gsnap_sse2-nr-x.o gsnap_sse2-knownsplicing.o gsnap_sse2-knownindels.o gsnap_sse2-splice.o gsnap_sse2-indel.o gsnap_sse2-spliceendsgen.o gsnap_sse2-spliceends.o gsnap_sse2-bitpack64-access.o gsnap_sse2-trdiag.o gsnap_sse2-trdiagpool.o gsnap_sse2-tr-extension-search.o gsnap_sse2-univdiag.o gsnap_sse2-univdiagpool.o gsnap_sse2-sedgesort.o gsnap_sse2-auxinfo.o gsnap_sse2-pathstore.o gsnap_sse2-altsplice.o gsnap_sse2-path.o gsnap_sse2-pathpair.o gsnap_sse2-path-solve.o gsnap_sse2-path-fusion.o gsnap_sse2-path-trim.o gsnap_sse2-path-eval.o gsnap_sse2-pathpair-eval.o gsnap_sse2-path-print-alignment.o gsnap_sse2-path-print-m8.o gsnap_sse2-path-print-sam.o gsnap_sse2-path-learn.o gsnap_sse2-method.o gsnap_sse2-doublelist.o gsnap_sse2-bitvector.o gsnap_sse2-transcriptpool.o gsnap_sse2-exon.o gsnap_sse2-transcript.o gsnap_sse2-trpathpool.o gsnap_sse2-trpath.o gsnap_sse2-trpath-solve.o gsnap_sse2-trpath-convert.o gsnap_sse2-trpath-eval.o gsnap_sse2-transcriptome-search.o gsnap_sse2-vectorpool.o gsnap_sse2-repair.o gsnap_sse2-transcript-remap.o gsnap_sse2-transcript-velocity.o gsnap_sse2-intersect-small.o gsnap_sse2-intersect-uint2.o gsnap_sse2-intersect-approx-uint4.o gsnap_sse2-intersect-approx-indices-uint4.o gsnap_sse2-intersect-wdups-indices.o gsnap_sse2-intersect-lower-small.o gsnap_sse2-intersect-higher-small.o gsnap_sse2-intersect-indices-small.o gsnap_sse2-intersect-indices2-small.o gsnap_sse2-intersect-concordance-uint4.o gsnap_sse2-kmer-search.o gsnap_sse2-extension-search.o gsnap_sse2-repetitive.o gsnap_sse2-uint8table.o gsnap_sse2-uinttable.o gsnap_sse2-stage1hr.o gsnap_sse2-stage1hr-single.o gsnap_sse2-stage1hr-paired.o gsnap_sse2-uinttableuint.o gsnap_sse2-tableuint.o gsnap_sse2-single-cell.o gsnap_sse2-request.o gsnap_sse2-resulthr.o gsnap_sse2-output.o gsnap_sse2-inbuffer.o gsnap_sse2-samheader.o gsnap_sse2-printbuffer.o gsnap_sse2-outbuffer.o gsnap_sse2-uintpairtable.o gsnap_sse2-splice-count.o gsnap_sse2-support.o gsnap_sse2-datadir.o gsnap_sse2-parserange.o gsnap_sse2-getline.o gsnap_sse2-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -msse2 -mno-ssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.sse2 gsnapl_sse2-except.o gsnapl_sse2-assert.o gsnapl_sse2-mem.o gsnapl_sse2-intlist.o gsnapl_sse2-uintlist.o gsnapl_sse2-uint8list.o gsnapl_sse2-list.o gsnapl_sse2-littleendian.o gsnapl_sse2-bigendian.o gsnapl_sse2-univinterval.o gsnapl_sse2-interval.o gsnapl_sse2-stopwatch.o gsnapl_sse2-semaphore.o gsnapl_sse2-access.o gsnapl_sse2-filestring.o gsnapl_sse2-iit-read-univ.o gsnapl_sse2-iit-read.o gsnapl_sse2-bzip2.o gsnapl_sse2-reader.o gsnapl_sse2-genomicpos.o gsnapl_sse2-compress.o gsnapl_sse2-genome.o gsnapl_sse2-transcriptome.o gsnapl_sse2-popcount.o gsnapl_sse2-genomebits.o gsnapl_sse2-genomebits_consec.o gsnapl_sse2-genomebits_count.o gsnapl_sse2-genomebits_kmer.o gsnapl_sse2-genomebits_indel.o gsnapl_sse2-genomebits_decode.o gsnapl_sse2-genomebits_mismatches.o gsnapl_sse2-genomebits_trim.o gsnapl_sse2-dinucl_bits.o gsnapl_sse2-genome_sites.o gsnapl_sse2-bitpack64-read.o gsnapl_sse2-bitpack64-readtwo.o gsnapl_sse2-mergeinfo.o gsnapl_sse2-merge-diagonals-heap-uint8.o gsnapl_sse2-merge-uint8.o gsnapl_sse2-merge-diagonals-simd-uint8.o gsnapl_sse2-merge-diagonals-heap-uint4.o gsnapl_sse2-merge-uint4.o gsnapl_sse2-merge-diagonals-simd-uint4.o gsnapl_sse2-indexdb.o gsnapl_sse2-localdb-read.o gsnapl_sse2-oligo.o gsnapl_sse2-chrnum.o gsnapl_sse2-maxent_hr.o gsnapl_sse2-mapq.o gsnapl_sse2-fopen.o gsnapl_sse2-shortread.o gsnapl_sse2-junction.o gsnapl_sse2-concordance.o gsnapl_sse2-simplepair.o gsnapl_sse2-orderstat.o gsnapl_sse2-intlistpool.o gsnapl_sse2-uintlistpool.o gsnapl_sse2-uint8listpool.o gsnapl_sse2-listpool.o gsnapl_sse2-hitlistpool.o gsnapl_sse2-pathpool.o gsnapl_sse2-auxinfopool.o gsnapl_sse2-pathstorepool.o gsnapl_sse2-intron.o gsnapl_sse2-gbuffer.o gsnapl_sse2-select64-common.o gsnapl_sse2-select64-ones.o gsnapl_sse2-select64-zeroes.o gsnapl_sse2-ef64.o gsnapl_sse2-nr-x.o gsnapl_sse2-knownsplicing.o gsnapl_sse2-knownindels.o gsnapl_sse2-splice.o gsnapl_sse2-indel.o gsnapl_sse2-spliceendsgen.o gsnapl_sse2-spliceends.o gsnapl_sse2-bitpack64-access.o gsnapl_sse2-trdiag.o gsnapl_sse2-trdiagpool.o gsnapl_sse2-tr-extension-search.o gsnapl_sse2-univdiag.o gsnapl_sse2-univdiagpool.o gsnapl_sse2-sedgesort.o gsnapl_sse2-auxinfo.o gsnapl_sse2-pathstore.o gsnapl_sse2-altsplice.o gsnapl_sse2-path.o gsnapl_sse2-pathpair.o gsnapl_sse2-path-solve.o gsnapl_sse2-path-fusion.o gsnapl_sse2-path-trim.o gsnapl_sse2-path-eval.o gsnapl_sse2-pathpair-eval.o gsnapl_sse2-path-print-alignment.o gsnapl_sse2-path-print-m8.o gsnapl_sse2-path-print-sam.o gsnapl_sse2-path-learn.o gsnapl_sse2-method.o gsnapl_sse2-doublelist.o gsnapl_sse2-bitvector.o gsnapl_sse2-transcriptpool.o gsnapl_sse2-exon.o gsnapl_sse2-transcript.o gsnapl_sse2-trpathpool.o gsnapl_sse2-trpath.o gsnapl_sse2-trpath-solve.o gsnapl_sse2-trpath-convert.o gsnapl_sse2-trpath-eval.o gsnapl_sse2-transcriptome-search.o gsnapl_sse2-vectorpool.o gsnapl_sse2-repair.o gsnapl_sse2-transcript-remap.o gsnapl_sse2-transcript-velocity.o gsnapl_sse2-intersect-large.o gsnapl_sse2-intersect-small.o gsnapl_sse2-intersect-uint2.o gsnapl_sse2-intersect-approx-uint4.o gsnapl_sse2-intersect-approx-uint8.o gsnapl_sse2-intersect-approx-indices-uint8.o gsnapl_sse2-intersect-wdups-indices.o gsnapl_sse2-intersect-lower-large.o gsnapl_sse2-intersect-higher-large.o gsnapl_sse2-intersect-indices-small.o gsnapl_sse2-intersect-indices2-large.o gsnapl_sse2-intersect-indices-uint8.o gsnapl_sse2-intersect-concordance-uint8.o gsnapl_sse2-kmer-search.o gsnapl_sse2-extension-search.o gsnapl_sse2-repetitive.o gsnapl_sse2-uint8table.o gsnapl_sse2-stage1hr.o gsnapl_sse2-stage1hr-single.o gsnapl_sse2-stage1hr-paired.o gsnapl_sse2-uint8tableuint.o gsnapl_sse2-tableuint.o gsnapl_sse2-single-cell.o gsnapl_sse2-request.o gsnapl_sse2-resulthr.o gsnapl_sse2-output.o gsnapl_sse2-inbuffer.o gsnapl_sse2-samheader.o gsnapl_sse2-printbuffer.o gsnapl_sse2-outbuffer.o gsnapl_sse2-uint8pairtable.o gsnapl_sse2-splice-count.o gsnapl_sse2-support.o gsnapl_sse2-datadir.o gsnapl_sse2-parserange.o gsnapl_sse2-getline.o gsnapl_sse2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_introns chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes chmod +x gtf_splicesites cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_introns chmod +x gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_introns chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' dh_auto_build --builddir build_ssse3 cd build_ssse3 && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-cat.c: In function ‘main’: ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmap_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gmapl_ssse3-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnap_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -c -o gsnapl_ssse3-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmap.ssse3 gmap_ssse3-except.o gmap_ssse3-assert.o gmap_ssse3-mem.o gmap_ssse3-intlist.o gmap_ssse3-uintlist.o gmap_ssse3-list.o gmap_ssse3-littleendian.o gmap_ssse3-bigendian.o gmap_ssse3-univinterval.o gmap_ssse3-interval.o gmap_ssse3-stopwatch.o gmap_ssse3-semaphore.o gmap_ssse3-access.o gmap_ssse3-filestring.o gmap_ssse3-iit-read-univ.o gmap_ssse3-iit-read.o gmap_ssse3-md5.o gmap_ssse3-bzip2.o gmap_ssse3-fopen.o gmap_ssse3-sequence.o gmap_ssse3-reader.o gmap_ssse3-genomicpos.o gmap_ssse3-compress.o gmap_ssse3-compress-write.o gmap_ssse3-gbuffer.o gmap_ssse3-genome.o gmap_ssse3-popcount.o gmap_ssse3-dinucl_bits.o gmap_ssse3-genome_canonical.o gmap_ssse3-genome-write.o gmap_ssse3-bitpack64-read.o gmap_ssse3-bitpack64-readtwo.o gmap_ssse3-indexdb.o gmap_ssse3-oligo.o gmap_ssse3-block.o gmap_ssse3-chrom.o gmap_ssse3-segmentpos.o gmap_ssse3-chrnum.o gmap_ssse3-uinttable_rh.o gmap_ssse3-gregion.o gmap_ssse3-match.o gmap_ssse3-matchpool.o gmap_ssse3-diagnostic.o gmap_ssse3-stage1.o gmap_ssse3-diag.o gmap_ssse3-diagpool.o gmap_ssse3-cmet.o gmap_ssse3-atoi.o gmap_ssse3-orderstat.o gmap_ssse3-oligoindex_hr.o gmap_ssse3-intron.o gmap_ssse3-maxent.o gmap_ssse3-maxent_hr.o gmap_ssse3-pair.o gmap_ssse3-pairpool.o gmap_ssse3-cellpool.o gmap_ssse3-stage2.o gmap_ssse3-doublelist.o gmap_ssse3-smooth.o gmap_ssse3-splicestringpool.o gmap_ssse3-splicetrie_build.o gmap_ssse3-splicetrie.o gmap_ssse3-boyer-moore.o gmap_ssse3-dynprog.o gmap_ssse3-dynprog_simd.o gmap_ssse3-dynprog_single.o gmap_ssse3-dynprog_genome.o gmap_ssse3-dynprog_cdna.o gmap_ssse3-dynprog_end.o gmap_ssse3-translation.o gmap_ssse3-pbinom.o gmap_ssse3-changepoint.o gmap_ssse3-stage3.o gmap_ssse3-request.o gmap_ssse3-result.o gmap_ssse3-output.o gmap_ssse3-inbuffer.o gmap_ssse3-samheader.o gmap_ssse3-printbuffer.o gmap_ssse3-outbuffer.o gmap_ssse3-chimera.o gmap_ssse3-datadir.o gmap_ssse3-parserange.o gmap_ssse3-getline.o gmap_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gmapl.ssse3 gmapl_ssse3-except.o gmapl_ssse3-assert.o gmapl_ssse3-mem.o gmapl_ssse3-intlist.o gmapl_ssse3-uintlist.o gmapl_ssse3-uint8list.o gmapl_ssse3-list.o gmapl_ssse3-littleendian.o gmapl_ssse3-bigendian.o gmapl_ssse3-univinterval.o gmapl_ssse3-interval.o gmapl_ssse3-stopwatch.o gmapl_ssse3-semaphore.o gmapl_ssse3-access.o gmapl_ssse3-filestring.o gmapl_ssse3-iit-read-univ.o gmapl_ssse3-iit-read.o gmapl_ssse3-md5.o gmapl_ssse3-bzip2.o gmapl_ssse3-fopen.o gmapl_ssse3-sequence.o gmapl_ssse3-reader.o gmapl_ssse3-genomicpos.o gmapl_ssse3-compress.o gmapl_ssse3-compress-write.o gmapl_ssse3-gbuffer.o gmapl_ssse3-genome.o gmapl_ssse3-popcount.o gmapl_ssse3-dinucl_bits.o gmapl_ssse3-genome_canonical.o gmapl_ssse3-genome-write.o gmapl_ssse3-bitpack64-read.o gmapl_ssse3-bitpack64-readtwo.o gmapl_ssse3-indexdb.o gmapl_ssse3-oligo.o gmapl_ssse3-block.o gmapl_ssse3-chrom.o gmapl_ssse3-segmentpos.o gmapl_ssse3-chrnum.o gmapl_ssse3-uinttable_rh.o gmapl_ssse3-uint8table_rh.o gmapl_ssse3-gregion.o gmapl_ssse3-match.o gmapl_ssse3-matchpool.o gmapl_ssse3-diagnostic.o gmapl_ssse3-stage1.o gmapl_ssse3-diag.o gmapl_ssse3-diagpool.o gmapl_ssse3-cmet.o gmapl_ssse3-atoi.o gmapl_ssse3-orderstat.o gmapl_ssse3-oligoindex_hr.o gmapl_ssse3-intron.o gmapl_ssse3-maxent.o gmapl_ssse3-maxent_hr.o gmapl_ssse3-pair.o gmapl_ssse3-pairpool.o gmapl_ssse3-cellpool.o gmapl_ssse3-stage2.o gmapl_ssse3-doublelist.o gmapl_ssse3-smooth.o gmapl_ssse3-splicestringpool.o gmapl_ssse3-splicetrie_build.o gmapl_ssse3-splicetrie.o gmapl_ssse3-boyer-moore.o gmapl_ssse3-dynprog.o gmapl_ssse3-dynprog_simd.o gmapl_ssse3-dynprog_single.o gmapl_ssse3-dynprog_genome.o gmapl_ssse3-dynprog_cdna.o gmapl_ssse3-dynprog_end.o gmapl_ssse3-translation.o gmapl_ssse3-pbinom.o gmapl_ssse3-changepoint.o gmapl_ssse3-stage3.o gmapl_ssse3-request.o gmapl_ssse3-result.o gmapl_ssse3-output.o gmapl_ssse3-inbuffer.o gmapl_ssse3-samheader.o gmapl_ssse3-printbuffer.o gmapl_ssse3-outbuffer.o gmapl_ssse3-chimera.o gmapl_ssse3-datadir.o gmapl_ssse3-parserange.o gmapl_ssse3-getline.o gmapl_ssse3-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnap.ssse3 gsnap_ssse3-except.o gsnap_ssse3-assert.o gsnap_ssse3-mem.o gsnap_ssse3-intlist.o gsnap_ssse3-uintlist.o gsnap_ssse3-list.o gsnap_ssse3-littleendian.o gsnap_ssse3-bigendian.o gsnap_ssse3-univinterval.o gsnap_ssse3-interval.o gsnap_ssse3-stopwatch.o gsnap_ssse3-semaphore.o gsnap_ssse3-access.o gsnap_ssse3-filestring.o gsnap_ssse3-iit-read-univ.o gsnap_ssse3-iit-read.o gsnap_ssse3-bzip2.o gsnap_ssse3-reader.o gsnap_ssse3-genomicpos.o gsnap_ssse3-compress.o gsnap_ssse3-genome.o gsnap_ssse3-transcriptome.o gsnap_ssse3-popcount.o gsnap_ssse3-genomebits.o gsnap_ssse3-genomebits_consec.o gsnap_ssse3-genomebits_count.o gsnap_ssse3-genomebits_kmer.o gsnap_ssse3-genomebits_indel.o gsnap_ssse3-genomebits_decode.o gsnap_ssse3-genomebits_mismatches.o gsnap_ssse3-genomebits_trim.o gsnap_ssse3-dinucl_bits.o gsnap_ssse3-genome_sites.o gsnap_ssse3-bitpack64-read.o gsnap_ssse3-bitpack64-readtwo.o gsnap_ssse3-mergeinfo.o gsnap_ssse3-merge-diagonals-heap-uint4.o gsnap_ssse3-merge-uint4.o gsnap_ssse3-merge-diagonals-simd-uint4.o gsnap_ssse3-indexdb.o gsnap_ssse3-localdb-read.o gsnap_ssse3-oligo.o gsnap_ssse3-chrnum.o gsnap_ssse3-maxent_hr.o gsnap_ssse3-mapq.o gsnap_ssse3-fopen.o gsnap_ssse3-shortread.o gsnap_ssse3-junction.o gsnap_ssse3-concordance.o gsnap_ssse3-simplepair.o gsnap_ssse3-orderstat.o gsnap_ssse3-intlistpool.o gsnap_ssse3-uintlistpool.o gsnap_ssse3-listpool.o gsnap_ssse3-hitlistpool.o gsnap_ssse3-pathpool.o gsnap_ssse3-auxinfopool.o gsnap_ssse3-pathstorepool.o gsnap_ssse3-intron.o gsnap_ssse3-gbuffer.o gsnap_ssse3-select64-common.o gsnap_ssse3-select64-ones.o gsnap_ssse3-select64-zeroes.o gsnap_ssse3-ef64.o gsnap_ssse3-nr-x.o gsnap_ssse3-knownsplicing.o gsnap_ssse3-knownindels.o gsnap_ssse3-splice.o gsnap_ssse3-indel.o gsnap_ssse3-spliceendsgen.o gsnap_ssse3-spliceends.o gsnap_ssse3-bitpack64-access.o gsnap_ssse3-trdiag.o gsnap_ssse3-trdiagpool.o gsnap_ssse3-tr-extension-search.o gsnap_ssse3-univdiag.o gsnap_ssse3-univdiagpool.o gsnap_ssse3-sedgesort.o gsnap_ssse3-auxinfo.o gsnap_ssse3-pathstore.o gsnap_ssse3-altsplice.o gsnap_ssse3-path.o gsnap_ssse3-pathpair.o gsnap_ssse3-path-solve.o gsnap_ssse3-path-fusion.o gsnap_ssse3-path-trim.o gsnap_ssse3-path-eval.o gsnap_ssse3-pathpair-eval.o gsnap_ssse3-path-print-alignment.o gsnap_ssse3-path-print-m8.o gsnap_ssse3-path-print-sam.o gsnap_ssse3-path-learn.o gsnap_ssse3-method.o gsnap_ssse3-doublelist.o gsnap_ssse3-bitvector.o gsnap_ssse3-transcriptpool.o gsnap_ssse3-exon.o gsnap_ssse3-transcript.o gsnap_ssse3-trpathpool.o gsnap_ssse3-trpath.o gsnap_ssse3-trpath-solve.o gsnap_ssse3-trpath-convert.o gsnap_ssse3-trpath-eval.o gsnap_ssse3-transcriptome-search.o gsnap_ssse3-vectorpool.o gsnap_ssse3-repair.o gsnap_ssse3-transcript-remap.o gsnap_ssse3-transcript-velocity.o gsnap_ssse3-intersect-small.o gsnap_ssse3-intersect-uint2.o gsnap_ssse3-intersect-approx-uint4.o gsnap_ssse3-intersect-approx-indices-uint4.o gsnap_ssse3-intersect-wdups-indices.o gsnap_ssse3-intersect-lower-small.o gsnap_ssse3-intersect-higher-small.o gsnap_ssse3-intersect-indices-small.o gsnap_ssse3-intersect-indices2-small.o gsnap_ssse3-intersect-concordance-uint4.o gsnap_ssse3-kmer-search.o gsnap_ssse3-extension-search.o gsnap_ssse3-repetitive.o gsnap_ssse3-uint8table.o gsnap_ssse3-uinttable.o gsnap_ssse3-stage1hr.o gsnap_ssse3-stage1hr-single.o gsnap_ssse3-stage1hr-paired.o gsnap_ssse3-uinttableuint.o gsnap_ssse3-tableuint.o gsnap_ssse3-single-cell.o gsnap_ssse3-request.o gsnap_ssse3-resulthr.o gsnap_ssse3-output.o gsnap_ssse3-inbuffer.o gsnap_ssse3-samheader.o gsnap_ssse3-printbuffer.o gsnap_ssse3-outbuffer.o gsnap_ssse3-uintpairtable.o gsnap_ssse3-splice-count.o gsnap_ssse3-support.o gsnap_ssse3-datadir.o gsnap_ssse3-parserange.o gsnap_ssse3-getline.o gsnap_ssse3-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -msse2 -mssse3 -mno-sse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -UHAVE_MM_EXTRACT_EPI64 -UHAVE_STTNI -Wl,-z,relro -Wl,-z,now -o gsnapl.ssse3 gsnapl_ssse3-except.o gsnapl_ssse3-assert.o gsnapl_ssse3-mem.o gsnapl_ssse3-intlist.o gsnapl_ssse3-uintlist.o gsnapl_ssse3-uint8list.o gsnapl_ssse3-list.o gsnapl_ssse3-littleendian.o gsnapl_ssse3-bigendian.o gsnapl_ssse3-univinterval.o gsnapl_ssse3-interval.o gsnapl_ssse3-stopwatch.o gsnapl_ssse3-semaphore.o gsnapl_ssse3-access.o gsnapl_ssse3-filestring.o gsnapl_ssse3-iit-read-univ.o gsnapl_ssse3-iit-read.o gsnapl_ssse3-bzip2.o gsnapl_ssse3-reader.o gsnapl_ssse3-genomicpos.o gsnapl_ssse3-compress.o gsnapl_ssse3-genome.o gsnapl_ssse3-transcriptome.o gsnapl_ssse3-popcount.o gsnapl_ssse3-genomebits.o gsnapl_ssse3-genomebits_consec.o gsnapl_ssse3-genomebits_count.o gsnapl_ssse3-genomebits_kmer.o gsnapl_ssse3-genomebits_indel.o gsnapl_ssse3-genomebits_decode.o gsnapl_ssse3-genomebits_mismatches.o gsnapl_ssse3-genomebits_trim.o gsnapl_ssse3-dinucl_bits.o gsnapl_ssse3-genome_sites.o gsnapl_ssse3-bitpack64-read.o gsnapl_ssse3-bitpack64-readtwo.o gsnapl_ssse3-mergeinfo.o gsnapl_ssse3-merge-diagonals-heap-uint8.o gsnapl_ssse3-merge-uint8.o gsnapl_ssse3-merge-diagonals-simd-uint8.o gsnapl_ssse3-merge-diagonals-heap-uint4.o gsnapl_ssse3-merge-uint4.o gsnapl_ssse3-merge-diagonals-simd-uint4.o gsnapl_ssse3-indexdb.o gsnapl_ssse3-localdb-read.o gsnapl_ssse3-oligo.o gsnapl_ssse3-chrnum.o gsnapl_ssse3-maxent_hr.o gsnapl_ssse3-mapq.o gsnapl_ssse3-fopen.o gsnapl_ssse3-shortread.o gsnapl_ssse3-junction.o gsnapl_ssse3-concordance.o gsnapl_ssse3-simplepair.o gsnapl_ssse3-orderstat.o gsnapl_ssse3-intlistpool.o gsnapl_ssse3-uintlistpool.o gsnapl_ssse3-uint8listpool.o gsnapl_ssse3-listpool.o gsnapl_ssse3-hitlistpool.o gsnapl_ssse3-pathpool.o gsnapl_ssse3-auxinfopool.o gsnapl_ssse3-pathstorepool.o gsnapl_ssse3-intron.o gsnapl_ssse3-gbuffer.o gsnapl_ssse3-select64-common.o gsnapl_ssse3-select64-ones.o gsnapl_ssse3-select64-zeroes.o gsnapl_ssse3-ef64.o gsnapl_ssse3-nr-x.o gsnapl_ssse3-knownsplicing.o gsnapl_ssse3-knownindels.o gsnapl_ssse3-splice.o gsnapl_ssse3-indel.o gsnapl_ssse3-spliceendsgen.o gsnapl_ssse3-spliceends.o gsnapl_ssse3-bitpack64-access.o gsnapl_ssse3-trdiag.o gsnapl_ssse3-trdiagpool.o gsnapl_ssse3-tr-extension-search.o gsnapl_ssse3-univdiag.o gsnapl_ssse3-univdiagpool.o gsnapl_ssse3-sedgesort.o gsnapl_ssse3-auxinfo.o gsnapl_ssse3-pathstore.o gsnapl_ssse3-altsplice.o gsnapl_ssse3-path.o gsnapl_ssse3-pathpair.o gsnapl_ssse3-path-solve.o gsnapl_ssse3-path-fusion.o gsnapl_ssse3-path-trim.o gsnapl_ssse3-path-eval.o gsnapl_ssse3-pathpair-eval.o gsnapl_ssse3-path-print-alignment.o gsnapl_ssse3-path-print-m8.o gsnapl_ssse3-path-print-sam.o gsnapl_ssse3-path-learn.o gsnapl_ssse3-method.o gsnapl_ssse3-doublelist.o gsnapl_ssse3-bitvector.o gsnapl_ssse3-transcriptpool.o gsnapl_ssse3-exon.o gsnapl_ssse3-transcript.o gsnapl_ssse3-trpathpool.o gsnapl_ssse3-trpath.o gsnapl_ssse3-trpath-solve.o gsnapl_ssse3-trpath-convert.o gsnapl_ssse3-trpath-eval.o gsnapl_ssse3-transcriptome-search.o gsnapl_ssse3-vectorpool.o gsnapl_ssse3-repair.o gsnapl_ssse3-transcript-remap.o gsnapl_ssse3-transcript-velocity.o gsnapl_ssse3-intersect-large.o gsnapl_ssse3-intersect-small.o gsnapl_ssse3-intersect-uint2.o gsnapl_ssse3-intersect-approx-uint4.o gsnapl_ssse3-intersect-approx-uint8.o gsnapl_ssse3-intersect-approx-indices-uint8.o gsnapl_ssse3-intersect-wdups-indices.o gsnapl_ssse3-intersect-lower-large.o gsnapl_ssse3-intersect-higher-large.o gsnapl_ssse3-intersect-indices-small.o gsnapl_ssse3-intersect-indices2-large.o gsnapl_ssse3-intersect-indices-uint8.o gsnapl_ssse3-intersect-concordance-uint8.o gsnapl_ssse3-kmer-search.o gsnapl_ssse3-extension-search.o gsnapl_ssse3-repetitive.o gsnapl_ssse3-uint8table.o gsnapl_ssse3-stage1hr.o gsnapl_ssse3-stage1hr-single.o gsnapl_ssse3-stage1hr-paired.o gsnapl_ssse3-uint8tableuint.o gsnapl_ssse3-tableuint.o gsnapl_ssse3-single-cell.o gsnapl_ssse3-request.o gsnapl_ssse3-resulthr.o gsnapl_ssse3-output.o gsnapl_ssse3-inbuffer.o gsnapl_ssse3-samheader.o gsnapl_ssse3-printbuffer.o gsnapl_ssse3-outbuffer.o gsnapl_ssse3-uint8pairtable.o gsnapl_ssse3-splice-count.o gsnapl_ssse3-support.o gsnapl_ssse3-datadir.o gsnapl_ssse3-parserange.o gsnapl_ssse3-getline.o gsnapl_ssse3-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords cp psl_introns.pl psl_introns chmod +x psl_splicesites chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' dh_auto_build --builddir build_sse41 cd build_sse41 && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-cat.c: In function ‘main’: ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse41-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse41-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse41 gmap_sse41-except.o gmap_sse41-assert.o gmap_sse41-mem.o gmap_sse41-intlist.o gmap_sse41-uintlist.o gmap_sse41-list.o gmap_sse41-littleendian.o gmap_sse41-bigendian.o gmap_sse41-univinterval.o gmap_sse41-interval.o gmap_sse41-stopwatch.o gmap_sse41-semaphore.o gmap_sse41-access.o gmap_sse41-filestring.o gmap_sse41-iit-read-univ.o gmap_sse41-iit-read.o gmap_sse41-md5.o gmap_sse41-bzip2.o gmap_sse41-fopen.o gmap_sse41-sequence.o gmap_sse41-reader.o gmap_sse41-genomicpos.o gmap_sse41-compress.o gmap_sse41-compress-write.o gmap_sse41-gbuffer.o gmap_sse41-genome.o gmap_sse41-popcount.o gmap_sse41-dinucl_bits.o gmap_sse41-genome_canonical.o gmap_sse41-genome-write.o gmap_sse41-bitpack64-read.o gmap_sse41-bitpack64-readtwo.o gmap_sse41-indexdb.o gmap_sse41-oligo.o gmap_sse41-block.o gmap_sse41-chrom.o gmap_sse41-segmentpos.o gmap_sse41-chrnum.o gmap_sse41-uinttable_rh.o gmap_sse41-gregion.o gmap_sse41-match.o gmap_sse41-matchpool.o gmap_sse41-diagnostic.o gmap_sse41-stage1.o gmap_sse41-diag.o gmap_sse41-diagpool.o gmap_sse41-cmet.o gmap_sse41-atoi.o gmap_sse41-orderstat.o gmap_sse41-oligoindex_hr.o gmap_sse41-intron.o gmap_sse41-maxent.o gmap_sse41-maxent_hr.o gmap_sse41-pair.o gmap_sse41-pairpool.o gmap_sse41-cellpool.o gmap_sse41-stage2.o gmap_sse41-doublelist.o gmap_sse41-smooth.o gmap_sse41-splicestringpool.o gmap_sse41-splicetrie_build.o gmap_sse41-splicetrie.o gmap_sse41-boyer-moore.o gmap_sse41-dynprog.o gmap_sse41-dynprog_simd.o gmap_sse41-dynprog_single.o gmap_sse41-dynprog_genome.o gmap_sse41-dynprog_cdna.o gmap_sse41-dynprog_end.o gmap_sse41-translation.o gmap_sse41-pbinom.o gmap_sse41-changepoint.o gmap_sse41-stage3.o gmap_sse41-request.o gmap_sse41-result.o gmap_sse41-output.o gmap_sse41-inbuffer.o gmap_sse41-samheader.o gmap_sse41-printbuffer.o gmap_sse41-outbuffer.o gmap_sse41-chimera.o gmap_sse41-datadir.o gmap_sse41-parserange.o gmap_sse41-getline.o gmap_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse41 gmapl_sse41-except.o gmapl_sse41-assert.o gmapl_sse41-mem.o gmapl_sse41-intlist.o gmapl_sse41-uintlist.o gmapl_sse41-uint8list.o gmapl_sse41-list.o gmapl_sse41-littleendian.o gmapl_sse41-bigendian.o gmapl_sse41-univinterval.o gmapl_sse41-interval.o gmapl_sse41-stopwatch.o gmapl_sse41-semaphore.o gmapl_sse41-access.o gmapl_sse41-filestring.o gmapl_sse41-iit-read-univ.o gmapl_sse41-iit-read.o gmapl_sse41-md5.o gmapl_sse41-bzip2.o gmapl_sse41-fopen.o gmapl_sse41-sequence.o gmapl_sse41-reader.o gmapl_sse41-genomicpos.o gmapl_sse41-compress.o gmapl_sse41-compress-write.o gmapl_sse41-gbuffer.o gmapl_sse41-genome.o gmapl_sse41-popcount.o gmapl_sse41-dinucl_bits.o gmapl_sse41-genome_canonical.o gmapl_sse41-genome-write.o gmapl_sse41-bitpack64-read.o gmapl_sse41-bitpack64-readtwo.o gmapl_sse41-indexdb.o gmapl_sse41-oligo.o gmapl_sse41-block.o gmapl_sse41-chrom.o gmapl_sse41-segmentpos.o gmapl_sse41-chrnum.o gmapl_sse41-uinttable_rh.o gmapl_sse41-uint8table_rh.o gmapl_sse41-gregion.o gmapl_sse41-match.o gmapl_sse41-matchpool.o gmapl_sse41-diagnostic.o gmapl_sse41-stage1.o gmapl_sse41-diag.o gmapl_sse41-diagpool.o gmapl_sse41-cmet.o gmapl_sse41-atoi.o gmapl_sse41-orderstat.o gmapl_sse41-oligoindex_hr.o gmapl_sse41-intron.o gmapl_sse41-maxent.o gmapl_sse41-maxent_hr.o gmapl_sse41-pair.o gmapl_sse41-pairpool.o gmapl_sse41-cellpool.o gmapl_sse41-stage2.o gmapl_sse41-doublelist.o gmapl_sse41-smooth.o gmapl_sse41-splicestringpool.o gmapl_sse41-splicetrie_build.o gmapl_sse41-splicetrie.o gmapl_sse41-boyer-moore.o gmapl_sse41-dynprog.o gmapl_sse41-dynprog_simd.o gmapl_sse41-dynprog_single.o gmapl_sse41-dynprog_genome.o gmapl_sse41-dynprog_cdna.o gmapl_sse41-dynprog_end.o gmapl_sse41-translation.o gmapl_sse41-pbinom.o gmapl_sse41-changepoint.o gmapl_sse41-stage3.o gmapl_sse41-request.o gmapl_sse41-result.o gmapl_sse41-output.o gmapl_sse41-inbuffer.o gmapl_sse41-samheader.o gmapl_sse41-printbuffer.o gmapl_sse41-outbuffer.o gmapl_sse41-chimera.o gmapl_sse41-datadir.o gmapl_sse41-parserange.o gmapl_sse41-getline.o gmapl_sse41-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse41 gsnap_sse41-except.o gsnap_sse41-assert.o gsnap_sse41-mem.o gsnap_sse41-intlist.o gsnap_sse41-uintlist.o gsnap_sse41-list.o gsnap_sse41-littleendian.o gsnap_sse41-bigendian.o gsnap_sse41-univinterval.o gsnap_sse41-interval.o gsnap_sse41-stopwatch.o gsnap_sse41-semaphore.o gsnap_sse41-access.o gsnap_sse41-filestring.o gsnap_sse41-iit-read-univ.o gsnap_sse41-iit-read.o gsnap_sse41-bzip2.o gsnap_sse41-reader.o gsnap_sse41-genomicpos.o gsnap_sse41-compress.o gsnap_sse41-genome.o gsnap_sse41-transcriptome.o gsnap_sse41-popcount.o gsnap_sse41-genomebits.o gsnap_sse41-genomebits_consec.o gsnap_sse41-genomebits_count.o gsnap_sse41-genomebits_kmer.o gsnap_sse41-genomebits_indel.o gsnap_sse41-genomebits_decode.o gsnap_sse41-genomebits_mismatches.o gsnap_sse41-genomebits_trim.o gsnap_sse41-dinucl_bits.o gsnap_sse41-genome_sites.o gsnap_sse41-bitpack64-read.o gsnap_sse41-bitpack64-readtwo.o gsnap_sse41-mergeinfo.o gsnap_sse41-merge-diagonals-heap-uint4.o gsnap_sse41-merge-uint4.o gsnap_sse41-merge-diagonals-simd-uint4.o gsnap_sse41-indexdb.o gsnap_sse41-localdb-read.o gsnap_sse41-oligo.o gsnap_sse41-chrnum.o gsnap_sse41-maxent_hr.o gsnap_sse41-mapq.o gsnap_sse41-fopen.o gsnap_sse41-shortread.o gsnap_sse41-junction.o gsnap_sse41-concordance.o gsnap_sse41-simplepair.o gsnap_sse41-orderstat.o gsnap_sse41-intlistpool.o gsnap_sse41-uintlistpool.o gsnap_sse41-listpool.o gsnap_sse41-hitlistpool.o gsnap_sse41-pathpool.o gsnap_sse41-auxinfopool.o gsnap_sse41-pathstorepool.o gsnap_sse41-intron.o gsnap_sse41-gbuffer.o gsnap_sse41-select64-common.o gsnap_sse41-select64-ones.o gsnap_sse41-select64-zeroes.o gsnap_sse41-ef64.o gsnap_sse41-nr-x.o gsnap_sse41-knownsplicing.o gsnap_sse41-knownindels.o gsnap_sse41-splice.o gsnap_sse41-indel.o gsnap_sse41-spliceendsgen.o gsnap_sse41-spliceends.o gsnap_sse41-bitpack64-access.o gsnap_sse41-trdiag.o gsnap_sse41-trdiagpool.o gsnap_sse41-tr-extension-search.o gsnap_sse41-univdiag.o gsnap_sse41-univdiagpool.o gsnap_sse41-sedgesort.o gsnap_sse41-auxinfo.o gsnap_sse41-pathstore.o gsnap_sse41-altsplice.o gsnap_sse41-path.o gsnap_sse41-pathpair.o gsnap_sse41-path-solve.o gsnap_sse41-path-fusion.o gsnap_sse41-path-trim.o gsnap_sse41-path-eval.o gsnap_sse41-pathpair-eval.o gsnap_sse41-path-print-alignment.o gsnap_sse41-path-print-m8.o gsnap_sse41-path-print-sam.o gsnap_sse41-path-learn.o gsnap_sse41-method.o gsnap_sse41-doublelist.o gsnap_sse41-bitvector.o gsnap_sse41-transcriptpool.o gsnap_sse41-exon.o gsnap_sse41-transcript.o gsnap_sse41-trpathpool.o gsnap_sse41-trpath.o gsnap_sse41-trpath-solve.o gsnap_sse41-trpath-convert.o gsnap_sse41-trpath-eval.o gsnap_sse41-transcriptome-search.o gsnap_sse41-vectorpool.o gsnap_sse41-repair.o gsnap_sse41-transcript-remap.o gsnap_sse41-transcript-velocity.o gsnap_sse41-intersect-small.o gsnap_sse41-intersect-uint2.o gsnap_sse41-intersect-approx-uint4.o gsnap_sse41-intersect-approx-indices-uint4.o gsnap_sse41-intersect-wdups-indices.o gsnap_sse41-intersect-lower-small.o gsnap_sse41-intersect-higher-small.o gsnap_sse41-intersect-indices-small.o gsnap_sse41-intersect-indices2-small.o gsnap_sse41-intersect-concordance-uint4.o gsnap_sse41-kmer-search.o gsnap_sse41-extension-search.o gsnap_sse41-repetitive.o gsnap_sse41-uint8table.o gsnap_sse41-uinttable.o gsnap_sse41-stage1hr.o gsnap_sse41-stage1hr-single.o gsnap_sse41-stage1hr-paired.o gsnap_sse41-uinttableuint.o gsnap_sse41-tableuint.o gsnap_sse41-single-cell.o gsnap_sse41-request.o gsnap_sse41-resulthr.o gsnap_sse41-output.o gsnap_sse41-inbuffer.o gsnap_sse41-samheader.o gsnap_sse41-printbuffer.o gsnap_sse41-outbuffer.o gsnap_sse41-uintpairtable.o gsnap_sse41-splice-count.o gsnap_sse41-support.o gsnap_sse41-datadir.o gsnap_sse41-parserange.o gsnap_sse41-getline.o gsnap_sse41-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -msse2 -mssse3 -msse4.1 -mno-sse4.2 -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse41 gsnapl_sse41-except.o gsnapl_sse41-assert.o gsnapl_sse41-mem.o gsnapl_sse41-intlist.o gsnapl_sse41-uintlist.o gsnapl_sse41-uint8list.o gsnapl_sse41-list.o gsnapl_sse41-littleendian.o gsnapl_sse41-bigendian.o gsnapl_sse41-univinterval.o gsnapl_sse41-interval.o gsnapl_sse41-stopwatch.o gsnapl_sse41-semaphore.o gsnapl_sse41-access.o gsnapl_sse41-filestring.o gsnapl_sse41-iit-read-univ.o gsnapl_sse41-iit-read.o gsnapl_sse41-bzip2.o gsnapl_sse41-reader.o gsnapl_sse41-genomicpos.o gsnapl_sse41-compress.o gsnapl_sse41-genome.o gsnapl_sse41-transcriptome.o gsnapl_sse41-popcount.o gsnapl_sse41-genomebits.o gsnapl_sse41-genomebits_consec.o gsnapl_sse41-genomebits_count.o gsnapl_sse41-genomebits_kmer.o gsnapl_sse41-genomebits_indel.o gsnapl_sse41-genomebits_decode.o gsnapl_sse41-genomebits_mismatches.o gsnapl_sse41-genomebits_trim.o gsnapl_sse41-dinucl_bits.o gsnapl_sse41-genome_sites.o gsnapl_sse41-bitpack64-read.o gsnapl_sse41-bitpack64-readtwo.o gsnapl_sse41-mergeinfo.o gsnapl_sse41-merge-diagonals-heap-uint8.o gsnapl_sse41-merge-uint8.o gsnapl_sse41-merge-diagonals-simd-uint8.o gsnapl_sse41-merge-diagonals-heap-uint4.o gsnapl_sse41-merge-uint4.o gsnapl_sse41-merge-diagonals-simd-uint4.o gsnapl_sse41-indexdb.o gsnapl_sse41-localdb-read.o gsnapl_sse41-oligo.o gsnapl_sse41-chrnum.o gsnapl_sse41-maxent_hr.o gsnapl_sse41-mapq.o gsnapl_sse41-fopen.o gsnapl_sse41-shortread.o gsnapl_sse41-junction.o gsnapl_sse41-concordance.o gsnapl_sse41-simplepair.o gsnapl_sse41-orderstat.o gsnapl_sse41-intlistpool.o gsnapl_sse41-uintlistpool.o gsnapl_sse41-uint8listpool.o gsnapl_sse41-listpool.o gsnapl_sse41-hitlistpool.o gsnapl_sse41-pathpool.o gsnapl_sse41-auxinfopool.o gsnapl_sse41-pathstorepool.o gsnapl_sse41-intron.o gsnapl_sse41-gbuffer.o gsnapl_sse41-select64-common.o gsnapl_sse41-select64-ones.o gsnapl_sse41-select64-zeroes.o gsnapl_sse41-ef64.o gsnapl_sse41-nr-x.o gsnapl_sse41-knownsplicing.o gsnapl_sse41-knownindels.o gsnapl_sse41-splice.o gsnapl_sse41-indel.o gsnapl_sse41-spliceendsgen.o gsnapl_sse41-spliceends.o gsnapl_sse41-bitpack64-access.o gsnapl_sse41-trdiag.o gsnapl_sse41-trdiagpool.o gsnapl_sse41-tr-extension-search.o gsnapl_sse41-univdiag.o gsnapl_sse41-univdiagpool.o gsnapl_sse41-sedgesort.o gsnapl_sse41-auxinfo.o gsnapl_sse41-pathstore.o gsnapl_sse41-altsplice.o gsnapl_sse41-path.o gsnapl_sse41-pathpair.o gsnapl_sse41-path-solve.o gsnapl_sse41-path-fusion.o gsnapl_sse41-path-trim.o gsnapl_sse41-path-eval.o gsnapl_sse41-pathpair-eval.o gsnapl_sse41-path-print-alignment.o gsnapl_sse41-path-print-m8.o gsnapl_sse41-path-print-sam.o gsnapl_sse41-path-learn.o gsnapl_sse41-method.o gsnapl_sse41-doublelist.o gsnapl_sse41-bitvector.o gsnapl_sse41-transcriptpool.o gsnapl_sse41-exon.o gsnapl_sse41-transcript.o gsnapl_sse41-trpathpool.o gsnapl_sse41-trpath.o gsnapl_sse41-trpath-solve.o gsnapl_sse41-trpath-convert.o gsnapl_sse41-trpath-eval.o gsnapl_sse41-transcriptome-search.o gsnapl_sse41-vectorpool.o gsnapl_sse41-repair.o gsnapl_sse41-transcript-remap.o gsnapl_sse41-transcript-velocity.o gsnapl_sse41-intersect-large.o gsnapl_sse41-intersect-small.o gsnapl_sse41-intersect-uint2.o gsnapl_sse41-intersect-approx-uint4.o gsnapl_sse41-intersect-approx-uint8.o gsnapl_sse41-intersect-approx-indices-uint8.o gsnapl_sse41-intersect-wdups-indices.o gsnapl_sse41-intersect-lower-large.o gsnapl_sse41-intersect-higher-large.o gsnapl_sse41-intersect-indices-small.o gsnapl_sse41-intersect-indices2-large.o gsnapl_sse41-intersect-indices-uint8.o gsnapl_sse41-intersect-concordance-uint8.o gsnapl_sse41-kmer-search.o gsnapl_sse41-extension-search.o gsnapl_sse41-repetitive.o gsnapl_sse41-uint8table.o gsnapl_sse41-stage1hr.o gsnapl_sse41-stage1hr-single.o gsnapl_sse41-stage1hr-paired.o gsnapl_sse41-uint8tableuint.o gsnapl_sse41-tableuint.o gsnapl_sse41-single-cell.o gsnapl_sse41-request.o gsnapl_sse41-resulthr.o gsnapl_sse41-output.o gsnapl_sse41-inbuffer.o gsnapl_sse41-samheader.o gsnapl_sse41-printbuffer.o gsnapl_sse41-outbuffer.o gsnapl_sse41-uint8pairtable.o gsnapl_sse41-splice-count.o gsnapl_sse41-support.o gsnapl_sse41-datadir.o gsnapl_sse41-parserange.o gsnapl_sse41-getline.o gsnapl_sse41-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat cp fa_coords.pl fa_coords chmod +x md_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns chmod +x psl_introns cp psl_genes.pl psl_genes cp ensembl_genes.pl ensembl_genes chmod +x psl_genes chmod +x ensembl_genes cp gtf_splicesites.pl gtf_splicesites cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites chmod +x gff3_introns cp gff3_genes.pl gff3_genes cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes chmod +x dbsnp_iit cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit chmod +x gvf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' dh_auto_build --builddir build_sse42 cd build_sse42 && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb-cat.c: In function ‘main’: ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_sse42-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_sse42-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.sse42 gmap_sse42-except.o gmap_sse42-assert.o gmap_sse42-mem.o gmap_sse42-intlist.o gmap_sse42-uintlist.o gmap_sse42-list.o gmap_sse42-littleendian.o gmap_sse42-bigendian.o gmap_sse42-univinterval.o gmap_sse42-interval.o gmap_sse42-stopwatch.o gmap_sse42-semaphore.o gmap_sse42-access.o gmap_sse42-filestring.o gmap_sse42-iit-read-univ.o gmap_sse42-iit-read.o gmap_sse42-md5.o gmap_sse42-bzip2.o gmap_sse42-fopen.o gmap_sse42-sequence.o gmap_sse42-reader.o gmap_sse42-genomicpos.o gmap_sse42-compress.o gmap_sse42-compress-write.o gmap_sse42-gbuffer.o gmap_sse42-genome.o gmap_sse42-popcount.o gmap_sse42-dinucl_bits.o gmap_sse42-genome_canonical.o gmap_sse42-genome-write.o gmap_sse42-bitpack64-read.o gmap_sse42-bitpack64-readtwo.o gmap_sse42-indexdb.o gmap_sse42-oligo.o gmap_sse42-block.o gmap_sse42-chrom.o gmap_sse42-segmentpos.o gmap_sse42-chrnum.o gmap_sse42-uinttable_rh.o gmap_sse42-gregion.o gmap_sse42-match.o gmap_sse42-matchpool.o gmap_sse42-diagnostic.o gmap_sse42-stage1.o gmap_sse42-diag.o gmap_sse42-diagpool.o gmap_sse42-cmet.o gmap_sse42-atoi.o gmap_sse42-orderstat.o gmap_sse42-oligoindex_hr.o gmap_sse42-intron.o gmap_sse42-maxent.o gmap_sse42-maxent_hr.o gmap_sse42-pair.o gmap_sse42-pairpool.o gmap_sse42-cellpool.o gmap_sse42-stage2.o gmap_sse42-doublelist.o gmap_sse42-smooth.o gmap_sse42-splicestringpool.o gmap_sse42-splicetrie_build.o gmap_sse42-splicetrie.o gmap_sse42-boyer-moore.o gmap_sse42-dynprog.o gmap_sse42-dynprog_simd.o gmap_sse42-dynprog_single.o gmap_sse42-dynprog_genome.o gmap_sse42-dynprog_cdna.o gmap_sse42-dynprog_end.o gmap_sse42-translation.o gmap_sse42-pbinom.o gmap_sse42-changepoint.o gmap_sse42-stage3.o gmap_sse42-request.o gmap_sse42-result.o gmap_sse42-output.o gmap_sse42-inbuffer.o gmap_sse42-samheader.o gmap_sse42-printbuffer.o gmap_sse42-outbuffer.o gmap_sse42-chimera.o gmap_sse42-datadir.o gmap_sse42-parserange.o gmap_sse42-getline.o gmap_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.sse42 gmapl_sse42-except.o gmapl_sse42-assert.o gmapl_sse42-mem.o gmapl_sse42-intlist.o gmapl_sse42-uintlist.o gmapl_sse42-uint8list.o gmapl_sse42-list.o gmapl_sse42-littleendian.o gmapl_sse42-bigendian.o gmapl_sse42-univinterval.o gmapl_sse42-interval.o gmapl_sse42-stopwatch.o gmapl_sse42-semaphore.o gmapl_sse42-access.o gmapl_sse42-filestring.o gmapl_sse42-iit-read-univ.o gmapl_sse42-iit-read.o gmapl_sse42-md5.o gmapl_sse42-bzip2.o gmapl_sse42-fopen.o gmapl_sse42-sequence.o gmapl_sse42-reader.o gmapl_sse42-genomicpos.o gmapl_sse42-compress.o gmapl_sse42-compress-write.o gmapl_sse42-gbuffer.o gmapl_sse42-genome.o gmapl_sse42-popcount.o gmapl_sse42-dinucl_bits.o gmapl_sse42-genome_canonical.o gmapl_sse42-genome-write.o gmapl_sse42-bitpack64-read.o gmapl_sse42-bitpack64-readtwo.o gmapl_sse42-indexdb.o gmapl_sse42-oligo.o gmapl_sse42-block.o gmapl_sse42-chrom.o gmapl_sse42-segmentpos.o gmapl_sse42-chrnum.o gmapl_sse42-uinttable_rh.o gmapl_sse42-uint8table_rh.o gmapl_sse42-gregion.o gmapl_sse42-match.o gmapl_sse42-matchpool.o gmapl_sse42-diagnostic.o gmapl_sse42-stage1.o gmapl_sse42-diag.o gmapl_sse42-diagpool.o gmapl_sse42-cmet.o gmapl_sse42-atoi.o gmapl_sse42-orderstat.o gmapl_sse42-oligoindex_hr.o gmapl_sse42-intron.o gmapl_sse42-maxent.o gmapl_sse42-maxent_hr.o gmapl_sse42-pair.o gmapl_sse42-pairpool.o gmapl_sse42-cellpool.o gmapl_sse42-stage2.o gmapl_sse42-doublelist.o gmapl_sse42-smooth.o gmapl_sse42-splicestringpool.o gmapl_sse42-splicetrie_build.o gmapl_sse42-splicetrie.o gmapl_sse42-boyer-moore.o gmapl_sse42-dynprog.o gmapl_sse42-dynprog_simd.o gmapl_sse42-dynprog_single.o gmapl_sse42-dynprog_genome.o gmapl_sse42-dynprog_cdna.o gmapl_sse42-dynprog_end.o gmapl_sse42-translation.o gmapl_sse42-pbinom.o gmapl_sse42-changepoint.o gmapl_sse42-stage3.o gmapl_sse42-request.o gmapl_sse42-result.o gmapl_sse42-output.o gmapl_sse42-inbuffer.o gmapl_sse42-samheader.o gmapl_sse42-printbuffer.o gmapl_sse42-outbuffer.o gmapl_sse42-chimera.o gmapl_sse42-datadir.o gmapl_sse42-parserange.o gmapl_sse42-getline.o gmapl_sse42-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.sse42 gsnap_sse42-except.o gsnap_sse42-assert.o gsnap_sse42-mem.o gsnap_sse42-intlist.o gsnap_sse42-uintlist.o gsnap_sse42-list.o gsnap_sse42-littleendian.o gsnap_sse42-bigendian.o gsnap_sse42-univinterval.o gsnap_sse42-interval.o gsnap_sse42-stopwatch.o gsnap_sse42-semaphore.o gsnap_sse42-access.o gsnap_sse42-filestring.o gsnap_sse42-iit-read-univ.o gsnap_sse42-iit-read.o gsnap_sse42-bzip2.o gsnap_sse42-reader.o gsnap_sse42-genomicpos.o gsnap_sse42-compress.o gsnap_sse42-genome.o gsnap_sse42-transcriptome.o gsnap_sse42-popcount.o gsnap_sse42-genomebits.o gsnap_sse42-genomebits_consec.o gsnap_sse42-genomebits_count.o gsnap_sse42-genomebits_kmer.o gsnap_sse42-genomebits_indel.o gsnap_sse42-genomebits_decode.o gsnap_sse42-genomebits_mismatches.o gsnap_sse42-genomebits_trim.o gsnap_sse42-dinucl_bits.o gsnap_sse42-genome_sites.o gsnap_sse42-bitpack64-read.o gsnap_sse42-bitpack64-readtwo.o gsnap_sse42-mergeinfo.o gsnap_sse42-merge-diagonals-heap-uint4.o gsnap_sse42-merge-uint4.o gsnap_sse42-merge-diagonals-simd-uint4.o gsnap_sse42-indexdb.o gsnap_sse42-localdb-read.o gsnap_sse42-oligo.o gsnap_sse42-chrnum.o gsnap_sse42-maxent_hr.o gsnap_sse42-mapq.o gsnap_sse42-fopen.o gsnap_sse42-shortread.o gsnap_sse42-junction.o gsnap_sse42-concordance.o gsnap_sse42-simplepair.o gsnap_sse42-orderstat.o gsnap_sse42-intlistpool.o gsnap_sse42-uintlistpool.o gsnap_sse42-listpool.o gsnap_sse42-hitlistpool.o gsnap_sse42-pathpool.o gsnap_sse42-auxinfopool.o gsnap_sse42-pathstorepool.o gsnap_sse42-intron.o gsnap_sse42-gbuffer.o gsnap_sse42-select64-common.o gsnap_sse42-select64-ones.o gsnap_sse42-select64-zeroes.o gsnap_sse42-ef64.o gsnap_sse42-nr-x.o gsnap_sse42-knownsplicing.o gsnap_sse42-knownindels.o gsnap_sse42-splice.o gsnap_sse42-indel.o gsnap_sse42-spliceendsgen.o gsnap_sse42-spliceends.o gsnap_sse42-bitpack64-access.o gsnap_sse42-trdiag.o gsnap_sse42-trdiagpool.o gsnap_sse42-tr-extension-search.o gsnap_sse42-univdiag.o gsnap_sse42-univdiagpool.o gsnap_sse42-sedgesort.o gsnap_sse42-auxinfo.o gsnap_sse42-pathstore.o gsnap_sse42-altsplice.o gsnap_sse42-path.o gsnap_sse42-pathpair.o gsnap_sse42-path-solve.o gsnap_sse42-path-fusion.o gsnap_sse42-path-trim.o gsnap_sse42-path-eval.o gsnap_sse42-pathpair-eval.o gsnap_sse42-path-print-alignment.o gsnap_sse42-path-print-m8.o gsnap_sse42-path-print-sam.o gsnap_sse42-path-learn.o gsnap_sse42-method.o gsnap_sse42-doublelist.o gsnap_sse42-bitvector.o gsnap_sse42-transcriptpool.o gsnap_sse42-exon.o gsnap_sse42-transcript.o gsnap_sse42-trpathpool.o gsnap_sse42-trpath.o gsnap_sse42-trpath-solve.o gsnap_sse42-trpath-convert.o gsnap_sse42-trpath-eval.o gsnap_sse42-transcriptome-search.o gsnap_sse42-vectorpool.o gsnap_sse42-repair.o gsnap_sse42-transcript-remap.o gsnap_sse42-transcript-velocity.o gsnap_sse42-intersect-small.o gsnap_sse42-intersect-uint2.o gsnap_sse42-intersect-approx-uint4.o gsnap_sse42-intersect-approx-indices-uint4.o gsnap_sse42-intersect-wdups-indices.o gsnap_sse42-intersect-lower-small.o gsnap_sse42-intersect-higher-small.o gsnap_sse42-intersect-indices-small.o gsnap_sse42-intersect-indices2-small.o gsnap_sse42-intersect-concordance-uint4.o gsnap_sse42-kmer-search.o gsnap_sse42-extension-search.o gsnap_sse42-repetitive.o gsnap_sse42-uint8table.o gsnap_sse42-uinttable.o gsnap_sse42-stage1hr.o gsnap_sse42-stage1hr-single.o gsnap_sse42-stage1hr-paired.o gsnap_sse42-uinttableuint.o gsnap_sse42-tableuint.o gsnap_sse42-single-cell.o gsnap_sse42-request.o gsnap_sse42-resulthr.o gsnap_sse42-output.o gsnap_sse42-inbuffer.o gsnap_sse42-samheader.o gsnap_sse42-printbuffer.o gsnap_sse42-outbuffer.o gsnap_sse42-uintpairtable.o gsnap_sse42-splice-count.o gsnap_sse42-support.o gsnap_sse42-datadir.o gsnap_sse42-parserange.o gsnap_sse42-getline.o gsnap_sse42-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mabm -mbmi -mno-avx2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.sse42 gsnapl_sse42-except.o gsnapl_sse42-assert.o gsnapl_sse42-mem.o gsnapl_sse42-intlist.o gsnapl_sse42-uintlist.o gsnapl_sse42-uint8list.o gsnapl_sse42-list.o gsnapl_sse42-littleendian.o gsnapl_sse42-bigendian.o gsnapl_sse42-univinterval.o gsnapl_sse42-interval.o gsnapl_sse42-stopwatch.o gsnapl_sse42-semaphore.o gsnapl_sse42-access.o gsnapl_sse42-filestring.o gsnapl_sse42-iit-read-univ.o gsnapl_sse42-iit-read.o gsnapl_sse42-bzip2.o gsnapl_sse42-reader.o gsnapl_sse42-genomicpos.o gsnapl_sse42-compress.o gsnapl_sse42-genome.o gsnapl_sse42-transcriptome.o gsnapl_sse42-popcount.o gsnapl_sse42-genomebits.o gsnapl_sse42-genomebits_consec.o gsnapl_sse42-genomebits_count.o gsnapl_sse42-genomebits_kmer.o gsnapl_sse42-genomebits_indel.o gsnapl_sse42-genomebits_decode.o gsnapl_sse42-genomebits_mismatches.o gsnapl_sse42-genomebits_trim.o gsnapl_sse42-dinucl_bits.o gsnapl_sse42-genome_sites.o gsnapl_sse42-bitpack64-read.o gsnapl_sse42-bitpack64-readtwo.o gsnapl_sse42-mergeinfo.o gsnapl_sse42-merge-diagonals-heap-uint8.o gsnapl_sse42-merge-uint8.o gsnapl_sse42-merge-diagonals-simd-uint8.o gsnapl_sse42-merge-diagonals-heap-uint4.o gsnapl_sse42-merge-uint4.o gsnapl_sse42-merge-diagonals-simd-uint4.o gsnapl_sse42-indexdb.o gsnapl_sse42-localdb-read.o gsnapl_sse42-oligo.o gsnapl_sse42-chrnum.o gsnapl_sse42-maxent_hr.o gsnapl_sse42-mapq.o gsnapl_sse42-fopen.o gsnapl_sse42-shortread.o gsnapl_sse42-junction.o gsnapl_sse42-concordance.o gsnapl_sse42-simplepair.o gsnapl_sse42-orderstat.o gsnapl_sse42-intlistpool.o gsnapl_sse42-uintlistpool.o gsnapl_sse42-uint8listpool.o gsnapl_sse42-listpool.o gsnapl_sse42-hitlistpool.o gsnapl_sse42-pathpool.o gsnapl_sse42-auxinfopool.o gsnapl_sse42-pathstorepool.o gsnapl_sse42-intron.o gsnapl_sse42-gbuffer.o gsnapl_sse42-select64-common.o gsnapl_sse42-select64-ones.o gsnapl_sse42-select64-zeroes.o gsnapl_sse42-ef64.o gsnapl_sse42-nr-x.o gsnapl_sse42-knownsplicing.o gsnapl_sse42-knownindels.o gsnapl_sse42-splice.o gsnapl_sse42-indel.o gsnapl_sse42-spliceendsgen.o gsnapl_sse42-spliceends.o gsnapl_sse42-bitpack64-access.o gsnapl_sse42-trdiag.o gsnapl_sse42-trdiagpool.o gsnapl_sse42-tr-extension-search.o gsnapl_sse42-univdiag.o gsnapl_sse42-univdiagpool.o gsnapl_sse42-sedgesort.o gsnapl_sse42-auxinfo.o gsnapl_sse42-pathstore.o gsnapl_sse42-altsplice.o gsnapl_sse42-path.o gsnapl_sse42-pathpair.o gsnapl_sse42-path-solve.o gsnapl_sse42-path-fusion.o gsnapl_sse42-path-trim.o gsnapl_sse42-path-eval.o gsnapl_sse42-pathpair-eval.o gsnapl_sse42-path-print-alignment.o gsnapl_sse42-path-print-m8.o gsnapl_sse42-path-print-sam.o gsnapl_sse42-path-learn.o gsnapl_sse42-method.o gsnapl_sse42-doublelist.o gsnapl_sse42-bitvector.o gsnapl_sse42-transcriptpool.o gsnapl_sse42-exon.o gsnapl_sse42-transcript.o gsnapl_sse42-trpathpool.o gsnapl_sse42-trpath.o gsnapl_sse42-trpath-solve.o gsnapl_sse42-trpath-convert.o gsnapl_sse42-trpath-eval.o gsnapl_sse42-transcriptome-search.o gsnapl_sse42-vectorpool.o gsnapl_sse42-repair.o gsnapl_sse42-transcript-remap.o gsnapl_sse42-transcript-velocity.o gsnapl_sse42-intersect-large.o gsnapl_sse42-intersect-small.o gsnapl_sse42-intersect-uint2.o gsnapl_sse42-intersect-approx-uint4.o gsnapl_sse42-intersect-approx-uint8.o gsnapl_sse42-intersect-approx-indices-uint8.o gsnapl_sse42-intersect-wdups-indices.o gsnapl_sse42-intersect-lower-large.o gsnapl_sse42-intersect-higher-large.o gsnapl_sse42-intersect-indices-small.o gsnapl_sse42-intersect-indices2-large.o gsnapl_sse42-intersect-indices-uint8.o gsnapl_sse42-intersect-concordance-uint8.o gsnapl_sse42-kmer-search.o gsnapl_sse42-extension-search.o gsnapl_sse42-repetitive.o gsnapl_sse42-uint8table.o gsnapl_sse42-stage1hr.o gsnapl_sse42-stage1hr-single.o gsnapl_sse42-stage1hr-paired.o gsnapl_sse42-uint8tableuint.o gsnapl_sse42-tableuint.o gsnapl_sse42-single-cell.o gsnapl_sse42-request.o gsnapl_sse42-resulthr.o gsnapl_sse42-output.o gsnapl_sse42-inbuffer.o gsnapl_sse42-samheader.o gsnapl_sse42-printbuffer.o gsnapl_sse42-outbuffer.o gsnapl_sse42-uint8pairtable.o gsnapl_sse42-splice-count.o gsnapl_sse42-support.o gsnapl_sse42-datadir.o gsnapl_sse42-parserange.o gsnapl_sse42-getline.o gsnapl_sse42-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat cp fa_coords.pl fa_coords chmod +x md_coords cp psl_splicesites.pl psl_splicesites chmod +x fa_coords chmod +x psl_splicesites cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_introns cp ensembl_genes.pl ensembl_genes chmod +x psl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites cp gtf_genes.pl gtf_genes chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes chmod +x gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_splicesites chmod +x gff3_genes cp dbsnp_iit.pl dbsnp_iit cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' dh_auto_build --builddir build_avx2 cd build_avx2 && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb-cat.c: In function ‘main’: ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx2-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx2-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx2 gmap_avx2-except.o gmap_avx2-assert.o gmap_avx2-mem.o gmap_avx2-intlist.o gmap_avx2-uintlist.o gmap_avx2-list.o gmap_avx2-littleendian.o gmap_avx2-bigendian.o gmap_avx2-univinterval.o gmap_avx2-interval.o gmap_avx2-stopwatch.o gmap_avx2-semaphore.o gmap_avx2-access.o gmap_avx2-filestring.o gmap_avx2-iit-read-univ.o gmap_avx2-iit-read.o gmap_avx2-md5.o gmap_avx2-bzip2.o gmap_avx2-fopen.o gmap_avx2-sequence.o gmap_avx2-reader.o gmap_avx2-genomicpos.o gmap_avx2-compress.o gmap_avx2-compress-write.o gmap_avx2-gbuffer.o gmap_avx2-genome.o gmap_avx2-popcount.o gmap_avx2-dinucl_bits.o gmap_avx2-genome_canonical.o gmap_avx2-genome-write.o gmap_avx2-bitpack64-read.o gmap_avx2-bitpack64-readtwo.o gmap_avx2-indexdb.o gmap_avx2-oligo.o gmap_avx2-block.o gmap_avx2-chrom.o gmap_avx2-segmentpos.o gmap_avx2-chrnum.o gmap_avx2-uinttable_rh.o gmap_avx2-gregion.o gmap_avx2-match.o gmap_avx2-matchpool.o gmap_avx2-diagnostic.o gmap_avx2-stage1.o gmap_avx2-diag.o gmap_avx2-diagpool.o gmap_avx2-cmet.o gmap_avx2-atoi.o gmap_avx2-orderstat.o gmap_avx2-oligoindex_hr.o gmap_avx2-intron.o gmap_avx2-maxent.o gmap_avx2-maxent_hr.o gmap_avx2-pair.o gmap_avx2-pairpool.o gmap_avx2-cellpool.o gmap_avx2-stage2.o gmap_avx2-doublelist.o gmap_avx2-smooth.o gmap_avx2-splicestringpool.o gmap_avx2-splicetrie_build.o gmap_avx2-splicetrie.o gmap_avx2-boyer-moore.o gmap_avx2-dynprog.o gmap_avx2-dynprog_simd.o gmap_avx2-dynprog_single.o gmap_avx2-dynprog_genome.o gmap_avx2-dynprog_cdna.o gmap_avx2-dynprog_end.o gmap_avx2-translation.o gmap_avx2-pbinom.o gmap_avx2-changepoint.o gmap_avx2-stage3.o gmap_avx2-request.o gmap_avx2-result.o gmap_avx2-output.o gmap_avx2-inbuffer.o gmap_avx2-samheader.o gmap_avx2-printbuffer.o gmap_avx2-outbuffer.o gmap_avx2-chimera.o gmap_avx2-datadir.o gmap_avx2-parserange.o gmap_avx2-getline.o gmap_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx2 gmapl_avx2-except.o gmapl_avx2-assert.o gmapl_avx2-mem.o gmapl_avx2-intlist.o gmapl_avx2-uintlist.o gmapl_avx2-uint8list.o gmapl_avx2-list.o gmapl_avx2-littleendian.o gmapl_avx2-bigendian.o gmapl_avx2-univinterval.o gmapl_avx2-interval.o gmapl_avx2-stopwatch.o gmapl_avx2-semaphore.o gmapl_avx2-access.o gmapl_avx2-filestring.o gmapl_avx2-iit-read-univ.o gmapl_avx2-iit-read.o gmapl_avx2-md5.o gmapl_avx2-bzip2.o gmapl_avx2-fopen.o gmapl_avx2-sequence.o gmapl_avx2-reader.o gmapl_avx2-genomicpos.o gmapl_avx2-compress.o gmapl_avx2-compress-write.o gmapl_avx2-gbuffer.o gmapl_avx2-genome.o gmapl_avx2-popcount.o gmapl_avx2-dinucl_bits.o gmapl_avx2-genome_canonical.o gmapl_avx2-genome-write.o gmapl_avx2-bitpack64-read.o gmapl_avx2-bitpack64-readtwo.o gmapl_avx2-indexdb.o gmapl_avx2-oligo.o gmapl_avx2-block.o gmapl_avx2-chrom.o gmapl_avx2-segmentpos.o gmapl_avx2-chrnum.o gmapl_avx2-uinttable_rh.o gmapl_avx2-uint8table_rh.o gmapl_avx2-gregion.o gmapl_avx2-match.o gmapl_avx2-matchpool.o gmapl_avx2-diagnostic.o gmapl_avx2-stage1.o gmapl_avx2-diag.o gmapl_avx2-diagpool.o gmapl_avx2-cmet.o gmapl_avx2-atoi.o gmapl_avx2-orderstat.o gmapl_avx2-oligoindex_hr.o gmapl_avx2-intron.o gmapl_avx2-maxent.o gmapl_avx2-maxent_hr.o gmapl_avx2-pair.o gmapl_avx2-pairpool.o gmapl_avx2-cellpool.o gmapl_avx2-stage2.o gmapl_avx2-doublelist.o gmapl_avx2-smooth.o gmapl_avx2-splicestringpool.o gmapl_avx2-splicetrie_build.o gmapl_avx2-splicetrie.o gmapl_avx2-boyer-moore.o gmapl_avx2-dynprog.o gmapl_avx2-dynprog_simd.o gmapl_avx2-dynprog_single.o gmapl_avx2-dynprog_genome.o gmapl_avx2-dynprog_cdna.o gmapl_avx2-dynprog_end.o gmapl_avx2-translation.o gmapl_avx2-pbinom.o gmapl_avx2-changepoint.o gmapl_avx2-stage3.o gmapl_avx2-request.o gmapl_avx2-result.o gmapl_avx2-output.o gmapl_avx2-inbuffer.o gmapl_avx2-samheader.o gmapl_avx2-printbuffer.o gmapl_avx2-outbuffer.o gmapl_avx2-chimera.o gmapl_avx2-datadir.o gmapl_avx2-parserange.o gmapl_avx2-getline.o gmapl_avx2-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx2 gsnap_avx2-except.o gsnap_avx2-assert.o gsnap_avx2-mem.o gsnap_avx2-intlist.o gsnap_avx2-uintlist.o gsnap_avx2-list.o gsnap_avx2-littleendian.o gsnap_avx2-bigendian.o gsnap_avx2-univinterval.o gsnap_avx2-interval.o gsnap_avx2-stopwatch.o gsnap_avx2-semaphore.o gsnap_avx2-access.o gsnap_avx2-filestring.o gsnap_avx2-iit-read-univ.o gsnap_avx2-iit-read.o gsnap_avx2-bzip2.o gsnap_avx2-reader.o gsnap_avx2-genomicpos.o gsnap_avx2-compress.o gsnap_avx2-genome.o gsnap_avx2-transcriptome.o gsnap_avx2-popcount.o gsnap_avx2-genomebits.o gsnap_avx2-genomebits_consec.o gsnap_avx2-genomebits_count.o gsnap_avx2-genomebits_kmer.o gsnap_avx2-genomebits_indel.o gsnap_avx2-genomebits_decode.o gsnap_avx2-genomebits_mismatches.o gsnap_avx2-genomebits_trim.o gsnap_avx2-dinucl_bits.o gsnap_avx2-genome_sites.o gsnap_avx2-bitpack64-read.o gsnap_avx2-bitpack64-readtwo.o gsnap_avx2-mergeinfo.o gsnap_avx2-merge-diagonals-heap-uint4.o gsnap_avx2-merge-uint4.o gsnap_avx2-merge-diagonals-simd-uint4.o gsnap_avx2-indexdb.o gsnap_avx2-localdb-read.o gsnap_avx2-oligo.o gsnap_avx2-chrnum.o gsnap_avx2-maxent_hr.o gsnap_avx2-mapq.o gsnap_avx2-fopen.o gsnap_avx2-shortread.o gsnap_avx2-junction.o gsnap_avx2-concordance.o gsnap_avx2-simplepair.o gsnap_avx2-orderstat.o gsnap_avx2-intlistpool.o gsnap_avx2-uintlistpool.o gsnap_avx2-listpool.o gsnap_avx2-hitlistpool.o gsnap_avx2-pathpool.o gsnap_avx2-auxinfopool.o gsnap_avx2-pathstorepool.o gsnap_avx2-intron.o gsnap_avx2-gbuffer.o gsnap_avx2-select64-common.o gsnap_avx2-select64-ones.o gsnap_avx2-select64-zeroes.o gsnap_avx2-ef64.o gsnap_avx2-nr-x.o gsnap_avx2-knownsplicing.o gsnap_avx2-knownindels.o gsnap_avx2-splice.o gsnap_avx2-indel.o gsnap_avx2-spliceendsgen.o gsnap_avx2-spliceends.o gsnap_avx2-bitpack64-access.o gsnap_avx2-trdiag.o gsnap_avx2-trdiagpool.o gsnap_avx2-tr-extension-search.o gsnap_avx2-univdiag.o gsnap_avx2-univdiagpool.o gsnap_avx2-sedgesort.o gsnap_avx2-auxinfo.o gsnap_avx2-pathstore.o gsnap_avx2-altsplice.o gsnap_avx2-path.o gsnap_avx2-pathpair.o gsnap_avx2-path-solve.o gsnap_avx2-path-fusion.o gsnap_avx2-path-trim.o gsnap_avx2-path-eval.o gsnap_avx2-pathpair-eval.o gsnap_avx2-path-print-alignment.o gsnap_avx2-path-print-m8.o gsnap_avx2-path-print-sam.o gsnap_avx2-path-learn.o gsnap_avx2-method.o gsnap_avx2-doublelist.o gsnap_avx2-bitvector.o gsnap_avx2-transcriptpool.o gsnap_avx2-exon.o gsnap_avx2-transcript.o gsnap_avx2-trpathpool.o gsnap_avx2-trpath.o gsnap_avx2-trpath-solve.o gsnap_avx2-trpath-convert.o gsnap_avx2-trpath-eval.o gsnap_avx2-transcriptome-search.o gsnap_avx2-vectorpool.o gsnap_avx2-repair.o gsnap_avx2-transcript-remap.o gsnap_avx2-transcript-velocity.o gsnap_avx2-intersect-small.o gsnap_avx2-intersect-uint2.o gsnap_avx2-intersect-approx-uint4.o gsnap_avx2-intersect-approx-indices-uint4.o gsnap_avx2-intersect-wdups-indices.o gsnap_avx2-intersect-lower-small.o gsnap_avx2-intersect-higher-small.o gsnap_avx2-intersect-indices-small.o gsnap_avx2-intersect-indices2-small.o gsnap_avx2-intersect-concordance-uint4.o gsnap_avx2-kmer-search.o gsnap_avx2-extension-search.o gsnap_avx2-repetitive.o gsnap_avx2-uint8table.o gsnap_avx2-uinttable.o gsnap_avx2-stage1hr.o gsnap_avx2-stage1hr-single.o gsnap_avx2-stage1hr-paired.o gsnap_avx2-uinttableuint.o gsnap_avx2-tableuint.o gsnap_avx2-single-cell.o gsnap_avx2-request.o gsnap_avx2-resulthr.o gsnap_avx2-output.o gsnap_avx2-inbuffer.o gsnap_avx2-samheader.o gsnap_avx2-printbuffer.o gsnap_avx2-outbuffer.o gsnap_avx2-uintpairtable.o gsnap_avx2-splice-count.o gsnap_avx2-support.o gsnap_avx2-datadir.o gsnap_avx2-parserange.o gsnap_avx2-getline.o gsnap_avx2-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mbmi2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx2 gsnapl_avx2-except.o gsnapl_avx2-assert.o gsnapl_avx2-mem.o gsnapl_avx2-intlist.o gsnapl_avx2-uintlist.o gsnapl_avx2-uint8list.o gsnapl_avx2-list.o gsnapl_avx2-littleendian.o gsnapl_avx2-bigendian.o gsnapl_avx2-univinterval.o gsnapl_avx2-interval.o gsnapl_avx2-stopwatch.o gsnapl_avx2-semaphore.o gsnapl_avx2-access.o gsnapl_avx2-filestring.o gsnapl_avx2-iit-read-univ.o gsnapl_avx2-iit-read.o gsnapl_avx2-bzip2.o gsnapl_avx2-reader.o gsnapl_avx2-genomicpos.o gsnapl_avx2-compress.o gsnapl_avx2-genome.o gsnapl_avx2-transcriptome.o gsnapl_avx2-popcount.o gsnapl_avx2-genomebits.o gsnapl_avx2-genomebits_consec.o gsnapl_avx2-genomebits_count.o gsnapl_avx2-genomebits_kmer.o gsnapl_avx2-genomebits_indel.o gsnapl_avx2-genomebits_decode.o gsnapl_avx2-genomebits_mismatches.o gsnapl_avx2-genomebits_trim.o gsnapl_avx2-dinucl_bits.o gsnapl_avx2-genome_sites.o gsnapl_avx2-bitpack64-read.o gsnapl_avx2-bitpack64-readtwo.o gsnapl_avx2-mergeinfo.o gsnapl_avx2-merge-diagonals-heap-uint8.o gsnapl_avx2-merge-uint8.o gsnapl_avx2-merge-diagonals-simd-uint8.o gsnapl_avx2-merge-diagonals-heap-uint4.o gsnapl_avx2-merge-uint4.o gsnapl_avx2-merge-diagonals-simd-uint4.o gsnapl_avx2-indexdb.o gsnapl_avx2-localdb-read.o gsnapl_avx2-oligo.o gsnapl_avx2-chrnum.o gsnapl_avx2-maxent_hr.o gsnapl_avx2-mapq.o gsnapl_avx2-fopen.o gsnapl_avx2-shortread.o gsnapl_avx2-junction.o gsnapl_avx2-concordance.o gsnapl_avx2-simplepair.o gsnapl_avx2-orderstat.o gsnapl_avx2-intlistpool.o gsnapl_avx2-uintlistpool.o gsnapl_avx2-uint8listpool.o gsnapl_avx2-listpool.o gsnapl_avx2-hitlistpool.o gsnapl_avx2-pathpool.o gsnapl_avx2-auxinfopool.o gsnapl_avx2-pathstorepool.o gsnapl_avx2-intron.o gsnapl_avx2-gbuffer.o gsnapl_avx2-select64-common.o gsnapl_avx2-select64-ones.o gsnapl_avx2-select64-zeroes.o gsnapl_avx2-ef64.o gsnapl_avx2-nr-x.o gsnapl_avx2-knownsplicing.o gsnapl_avx2-knownindels.o gsnapl_avx2-splice.o gsnapl_avx2-indel.o gsnapl_avx2-spliceendsgen.o gsnapl_avx2-spliceends.o gsnapl_avx2-bitpack64-access.o gsnapl_avx2-trdiag.o gsnapl_avx2-trdiagpool.o gsnapl_avx2-tr-extension-search.o gsnapl_avx2-univdiag.o gsnapl_avx2-univdiagpool.o gsnapl_avx2-sedgesort.o gsnapl_avx2-auxinfo.o gsnapl_avx2-pathstore.o gsnapl_avx2-altsplice.o gsnapl_avx2-path.o gsnapl_avx2-pathpair.o gsnapl_avx2-path-solve.o gsnapl_avx2-path-fusion.o gsnapl_avx2-path-trim.o gsnapl_avx2-path-eval.o gsnapl_avx2-pathpair-eval.o gsnapl_avx2-path-print-alignment.o gsnapl_avx2-path-print-m8.o gsnapl_avx2-path-print-sam.o gsnapl_avx2-path-learn.o gsnapl_avx2-method.o gsnapl_avx2-doublelist.o gsnapl_avx2-bitvector.o gsnapl_avx2-transcriptpool.o gsnapl_avx2-exon.o gsnapl_avx2-transcript.o gsnapl_avx2-trpathpool.o gsnapl_avx2-trpath.o gsnapl_avx2-trpath-solve.o gsnapl_avx2-trpath-convert.o gsnapl_avx2-trpath-eval.o gsnapl_avx2-transcriptome-search.o gsnapl_avx2-vectorpool.o gsnapl_avx2-repair.o gsnapl_avx2-transcript-remap.o gsnapl_avx2-transcript-velocity.o gsnapl_avx2-intersect-large.o gsnapl_avx2-intersect-small.o gsnapl_avx2-intersect-uint2.o gsnapl_avx2-intersect-approx-uint4.o gsnapl_avx2-intersect-approx-uint8.o gsnapl_avx2-intersect-approx-indices-uint8.o gsnapl_avx2-intersect-wdups-indices.o gsnapl_avx2-intersect-lower-large.o gsnapl_avx2-intersect-higher-large.o gsnapl_avx2-intersect-indices-small.o gsnapl_avx2-intersect-indices2-large.o gsnapl_avx2-intersect-indices-uint8.o gsnapl_avx2-intersect-concordance-uint8.o gsnapl_avx2-kmer-search.o gsnapl_avx2-extension-search.o gsnapl_avx2-repetitive.o gsnapl_avx2-uint8table.o gsnapl_avx2-stage1hr.o gsnapl_avx2-stage1hr-single.o gsnapl_avx2-stage1hr-paired.o gsnapl_avx2-uint8tableuint.o gsnapl_avx2-tableuint.o gsnapl_avx2-single-cell.o gsnapl_avx2-request.o gsnapl_avx2-resulthr.o gsnapl_avx2-output.o gsnapl_avx2-inbuffer.o gsnapl_avx2-samheader.o gsnapl_avx2-printbuffer.o gsnapl_avx2-outbuffer.o gsnapl_avx2-uint8pairtable.o gsnapl_avx2-splice-count.o gsnapl_avx2-support.o gsnapl_avx2-datadir.o gsnapl_avx2-parserange.o gsnapl_avx2-getline.o gsnapl_avx2-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_build chmod +x gmap_process cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites chmod +x fa_coords cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_genes chmod +x psl_introns cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns cp gtf_genes.pl gtf_genes chmod +x gtf_genes chmod +x gtf_introns cp gtf_transcript_splicesites.pl gtf_transcript_splicesites cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites cp gff3_introns.pl gff3_introns chmod +x gff3_splicesites cp gff3_genes.pl gff3_genes chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit chmod +x gff3_genes cp gvf_iit.pl gvf_iit chmod +x dbsnp_iit chmod +x gvf_iit cp vcf_iit.pl vcf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' dh_auto_build --builddir build_avx512 cd build_avx512 && make -j2 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' Making all in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' make all-am make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cpuid-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap-gmap_select.o `test -f 'gmap_select.c' || echo '../../src/'`gmap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl-gmapl_select.o `test -f 'gmapl_select.c' || echo '../../src/'`gmapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o get_genome-get-genome.o `test -f 'get-genome.c' || echo '../../src/'`get-genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-saca-k.o `test -f 'saca-k.c' || echo '../../src/'`saca-k.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-localdb-write.o `test -f 'localdb-write.c' || echo '../../src/'`localdb-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableuint8.o `test -f 'tableuint8.c' || echo '../../src/'`tableuint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-bytecoding.o `test -f 'bytecoding.c' || echo '../../src/'`bytecoding.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-sarray-write.o `test -f 'sarray-write.c' || echo '../../src/'`sarray-write.c In file included from ../../src/sarray-write.c:34: ../../src/sarray-write.c: In function ‘Sarray_write_csa’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:808:3: note: in expansion of macro ‘FREAD_UINT’ 808 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:815:5: note: in expansion of macro ‘FREAD_UINTS’ 815 | FREAD_UINTS(read_buffer,RW_BATCH,sa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:828:5: note: in expansion of macro ‘FREAD_UINT’ 828 | FREAD_UINT(&sa_i,sa_fp); | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1022:5: note: in expansion of macro ‘FREAD_UINTS’ 1022 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1033:5: note: in expansion of macro ‘FREAD_UINT’ 1033 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1064:5: note: in expansion of macro ‘FREAD_UINTS’ 1064 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1080:5: note: in expansion of macro ‘FREAD_UINT’ 1080 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1111:5: note: in expansion of macro ‘FREAD_UINTS’ 1111 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1112:5: note: in expansion of macro ‘FREAD_UINTS’ 1112 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1140:5: note: in expansion of macro ‘FREAD_UINT’ 1140 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1141:5: note: in expansion of macro ‘FREAD_UINT’ 1141 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_compute_lcp_bytes’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1246:5: note: in expansion of macro ‘FREAD_UINTS’ 1246 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1257:5: note: in expansion of macro ‘FREAD_UINT’ 1257 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1288:5: note: in expansion of macro ‘FREAD_UINTS’ 1288 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1304:5: note: in expansion of macro ‘FREAD_UINT’ 1304 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1335:5: note: in expansion of macro ‘FREAD_UINTS’ 1335 | FREAD_UINTS(read_buffer_1,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1336:5: note: in expansion of macro ‘FREAD_UINTS’ 1336 | FREAD_UINTS(read_buffer_2,RW_BATCH,permsa_fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1370:5: note: in expansion of macro ‘FREAD_UINT’ 1370 | FREAD_UINT(&rank_i,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:1371:5: note: in expansion of macro ‘FREAD_UINT’ 1371 | FREAD_UINT(&j,permsa_fp); /* j = SA[rank_i - 1] */ | ^~~~~~~~~~ ../../src/sarray-write.c: In function ‘Sarray_discriminating_chars’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2318:3: note: in expansion of macro ‘FREAD_UINT’ 2318 | FREAD_UINT(&SA_i_minus_1,fp); /* Initializes SA[0] */ | ^~~~~~~~~~ ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2321:5: note: in expansion of macro ‘FREAD_UINTS’ 2321 | FREAD_UINTS(read_buffer,RW_BATCH,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/sarray-write.c:2443:5: note: in expansion of macro ‘FREAD_UINT’ 2443 | FREAD_UINT(&SA_i,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapindex-gmapindex.o `test -f 'gmapindex.c' || echo '../../src/'`gmapindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o indexdb_cat-indexdb-cat.o `test -f 'indexdb-cat.c' || echo '../../src/'`indexdb-cat.c ../../src/indexdb-cat.c: In function ‘main’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/indexdb-cat.c:823:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 823 | fprintf(stderr,"Total number of offsets: %llu => pages file not required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:827:49: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 827 | fprintf(stderr,"Total number of offsets: %llu => pages file required\n",total_noffsets); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/indexdb-cat.c:901:14: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu ../../src/indexdb-cat.c:901:19: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 901 | printf("%llu %llu\n",total_noffsets,total_genomelength); | ~~~^ ~~~~~~~~~~~~~~~~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write-univ.o `test -f 'iit-write-univ.c' || echo '../../src/'`iit-write-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit-write.o `test -f 'iit-write.c' || echo '../../src/'`iit-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-tableint.o `test -f 'tableint.c' || echo '../../src/'`tableint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-table.o `test -f 'table.c' || echo '../../src/'`table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_store-iit_store.o `test -f 'iit_store.c' || echo '../../src/'`iit_store.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-except.o `test -f 'except.c' || echo '../../src/'`except.c ../../src/iit_store.c: In function ‘parse_fasta’: ../../src/iit_store.c:689:36: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 689 | fprintf(stderr,"Assigning %llu to end\n",end); | ~~~^ ~~~ | | | | | Univcoord_T {aka long unsigned int} | long long unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_get-iit_get.o `test -f 'iit_get.c' || echo '../../src/'`iit_get.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o iit_dump-iit_dump.o `test -f 'iit_dump.c' || echo '../../src/'`iit_dump.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap-gsnap_select.o `test -f 'gsnap_select.c' || echo '../../src/'`gsnap_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-cpuid.o `test -f 'cpuid.c' || echo '../../src/'`cpuid.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl-gsnapl_select.o `test -f 'gsnapl_select.c' || echo '../../src/'`gsnapl_select.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o snpindex-snpindex.o `test -f 'snpindex.c' || echo '../../src/'`snpindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o cmetindex-cmetindex.o `test -f 'cmetindex.c' || echo '../../src/'`cmetindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-incr.o `test -f 'bitpack64-incr.c' || echo '../../src/'`bitpack64-incr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-indexdb-write.o `test -f 'indexdb-write.c' || echo '../../src/'`indexdb-write.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets’: ../../src/indexdb-write.c:787:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 787 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_offsets_huge’: ../../src/indexdb-write.c:1179:30: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘long unsigned int’ [-Wformat=] 1179 | fprintf(stderr,"Writing %llu offsets compressed via bitpack64...",oligospace+1UL); | ~~~^ ~~~~~~~~~~~~~~ | | | | long long unsigned int long unsigned int | %lu ../../src/indexdb-write.c: In function ‘Indexdb_write_positions_huge_offsets’: ../../src/indexdb-write.c:2867:43: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Hugepositionsptr_T’ {aka ‘long unsigned int’} [-Wformat=] 2867 | fprintf(stderr,"Trying to allocate %llu*(%d+%d) bytes of memory for positions...", | ~~~^ | | | long long unsigned int | %lu 2868 | totalcounts,(int) sizeof(unsigned char),(int) sizeof(UINT8)); | ~~~~~~~~~~~ | | | Hugepositionsptr_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o atoiindex-atoiindex.o `test -f 'atoiindex.c' || echo '../../src/'`atoiindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-write.o `test -f 'bitpack64-write.c' || echo '../../src/'`bitpack64-write.c ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge’: ../../src/bitpack64-write.c:5396:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5396:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5396:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5396:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5396 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5397 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5424:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5424:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5424:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5424 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5425 | positioni,positioni/BLOCKSIZE,ascending[positioni],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5458:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5458:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5458:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5458 | fprintf(stderr,"\nAt final oligo %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5459 | n,n/BLOCKSIZE,ascending[n],nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c: In function ‘Bitpack64_write_differential_huge_bitpacks’: ../../src/bitpack64-write.c:5574:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5574:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5574:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5574:86: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5574 | fprintf(stderr,"\nAt position %llu (block %llu), ascending %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5575 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:40: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5603:52: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5603:70: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5603:87: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5603 | fprintf(stderr,"\nAt position %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5604 | positioni,positioni/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:41: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 3 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~ | | | Oligospace_T {aka long unsigned int} ../../src/bitpack64-write.c:5645:53: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Oligospace_T’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu ../../src/bitpack64-write.c:5645:71: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 5 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~~~ | | | UINT8 {aka long unsigned int} ../../src/bitpack64-write.c:5645:88: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 6 has type ‘UINT8’ {aka ‘long unsigned int’} [-Wformat=] 5645 | fprintf(stderr,"\nAt final oligo %llu (block %llu), totalcount %llu >= nextpage %llu", | ~~~^ | | | long long unsigned int | %lu 5646 | n,n/BLOCKSIZE,totalcount,nextpage); | ~~~~~~~~ | | | UINT8 {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o trindex-trindex.o `test -f 'trindex.c' || echo '../../src/'`trindex.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_nosimd-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-support.o `test -f 'support.c' || echo '../../src/'`support.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_nosimd-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmap_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-md5.o `test -f 'md5.c' || echo '../../src/'`md5.c In function ‘update’, inlined from ‘finish’ at ../../src/md5.c:241:3, inlined from ‘MD5_compute’ at ../../src/md5.c:273:10: ../../src/md5.c:212:7: warning: ‘transform’ accessing 64 bytes in a region of size 7 [-Wstringop-overflow=] 212 | transform(state,&(input[i])); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/md5.c:212:7: note: referencing argument 2 of type ‘unsigned char[64]’ ../../src/md5.c: In function ‘MD5_compute’: ../../src/md5.c:104:1: note: in a call to function ‘transform’ 104 | transform (UINT4 state[4], unsigned char block[64]) { | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-sequence.o `test -f 'sequence.c' || echo '../../src/'`sequence.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-compress-write.o `test -f 'compress-write.c' || echo '../../src/'`compress-write.c ../../src/compress-write.c: In function ‘put_compressed_one’: ../../src/compress-write.c:321:69: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 321 | fprintf(stderr,"Don't recognize character %c at position %llu. Using N instead\n",Buffer[i],position+i); | ~~~^ ~~~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/compress-write.c: In function ‘Compress_compress’: ../../src/compress-write.c:588:73: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 588 | fprintf(stderr,"Non-standard nucleotide %c at position %llu. Using N instead\n",c,position); | ~~~^ ~~~~~~~~ | | | | long long unsigned int Univcoord_T {aka long unsigned int} | %lu In file included from ../../src/compress-write.c:21: ../../src/compress-write.c: In function ‘Compress_cat’: ../../src/littleendian.h:26:29: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 26 | #define FREAD_UINTS(a,n,fp) fread(a,sizeof(UINT4),n,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/compress-write.c:847:5: note: in expansion of macro ‘FREAD_UINTS’ 847 | FREAD_UINTS(Buffer,3,fp); | ^~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome_canonical.o `test -f 'genome_canonical.c' || echo '../../src/'`genome_canonical.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-genome-write.o `test -f 'genome-write.c' || echo '../../src/'`genome-write.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-block.o `test -f 'block.c' || echo '../../src/'`block.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrom.o `test -f 'chrom.c' || echo '../../src/'`chrom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-segmentpos.o `test -f 'segmentpos.c' || echo '../../src/'`segmentpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uinttable_rh.o `test -f 'uinttable_rh.c' || echo '../../src/'`uinttable_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-uint8table_rh.o `test -f 'uint8table_rh.c' || echo '../../src/'`uint8table_rh.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gregion.o `test -f 'gregion.c' || echo '../../src/'`gregion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-match.o `test -f 'match.c' || echo '../../src/'`match.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-matchpool.o `test -f 'matchpool.c' || echo '../../src/'`matchpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagnostic.o `test -f 'diagnostic.c' || echo '../../src/'`diagnostic.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage1.o `test -f 'stage1.c' || echo '../../src/'`stage1.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diag.o `test -f 'diag.c' || echo '../../src/'`diag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-diagpool.o `test -f 'diagpool.c' || echo '../../src/'`diagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cmet.o `test -f 'cmet.c' || echo '../../src/'`cmet.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-atoi.o `test -f 'atoi.c' || echo '../../src/'`atoi.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-oligoindex_hr.o `test -f 'oligoindex_hr.c' || echo '../../src/'`oligoindex_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent.o `test -f 'maxent.c' || echo '../../src/'`maxent.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pair.o `test -f 'pair.c' || echo '../../src/'`pair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pairpool.o `test -f 'pairpool.c' || echo '../../src/'`pairpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-cellpool.o `test -f 'cellpool.c' || echo '../../src/'`cellpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage2.o `test -f 'stage2.c' || echo '../../src/'`stage2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-smooth.o `test -f 'smooth.c' || echo '../../src/'`smooth.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicestringpool.o `test -f 'splicestringpool.c' || echo '../../src/'`splicestringpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie_build.o `test -f 'splicetrie_build.c' || echo '../../src/'`splicetrie_build.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-splicetrie.o `test -f 'splicetrie.c' || echo '../../src/'`splicetrie.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-boyer-moore.o `test -f 'boyer-moore.c' || echo '../../src/'`boyer-moore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog.o `test -f 'dynprog.c' || echo '../../src/'`dynprog.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_simd.o `test -f 'dynprog_simd.c' || echo '../../src/'`dynprog_simd.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_single.o `test -f 'dynprog_single.c' || echo '../../src/'`dynprog_single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_genome.o `test -f 'dynprog_genome.c' || echo '../../src/'`dynprog_genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_cdna.o `test -f 'dynprog_cdna.c' || echo '../../src/'`dynprog_cdna.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-dynprog_end.o `test -f 'dynprog_end.c' || echo '../../src/'`dynprog_end.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-translation.o `test -f 'translation.c' || echo '../../src/'`translation.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-pbinom.o `test -f 'pbinom.c' || echo '../../src/'`pbinom.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-changepoint.o `test -f 'changepoint.c' || echo '../../src/'`changepoint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-stage3.o `test -f 'stage3.c' || echo '../../src/'`stage3.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-result.o `test -f 'result.c' || echo '../../src/'`result.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-chimera.o `test -f 'chimera.c' || echo '../../src/'`chimera.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gmapl_avx512-gmap.o `test -f 'gmap.c' || echo '../../src/'`gmap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple’: ../../src/indexdb.c:1953:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1953 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-approx-indices-uint4.o `test -f 'intersect-approx-indices-uint4.c' || echo '../../src/'`intersect-approx-indices-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-lower-small.o `test -f 'intersect-lower-small.c' || echo '../../src/'`intersect-lower-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-higher-small.o `test -f 'intersect-higher-small.c' || echo '../../src/'`intersect-higher-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-indices2-small.o `test -f 'intersect-indices2-small.c' || echo '../../src/'`intersect-indices2-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-intersect-concordance-uint4.o `test -f 'intersect-concordance-uint4.c' || echo '../../src/'`intersect-concordance-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttable.o `test -f 'uinttable.c' || echo '../../src/'`uinttable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uinttableuint.o `test -f 'uinttableuint.c' || echo '../../src/'`uinttableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-uintpairtable.o `test -f 'uintpairtable.c' || echo '../../src/'`uintpairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnap_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-except.o `test -f 'except.c' || echo '../../src/'`except.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-assert.o `test -f 'assert.c' || echo '../../src/'`assert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mem.o `test -f 'mem.c' || echo '../../src/'`mem.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlist.o `test -f 'intlist.c' || echo '../../src/'`intlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlist.o `test -f 'uintlist.c' || echo '../../src/'`uintlist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8list.o `test -f 'uint8list.c' || echo '../../src/'`uint8list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-list.o `test -f 'list.c' || echo '../../src/'`list.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-littleendian.o `test -f 'littleendian.c' || echo '../../src/'`littleendian.c ../../src/littleendian.c: In function ‘Littleendian_write_char’: ../../src/littleendian.c:14:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 14 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint’: ../../src/littleendian.c:27:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 27 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8’: ../../src/littleendian.c:45:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 45 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c: In function ‘Littleendian_write_uint8_as_uint’: ../../src/littleendian.c:60:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/littleendian.c:66:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bigendian.o `test -f 'bigendian.c' || echo '../../src/'`bigendian.c ../../src/bigendian.c: In function ‘Bigendian_write_char’: ../../src/bigendian.c:16:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 16 | write(fd,buf,1); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint’: ../../src/bigendian.c:215:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 215 | write(fd,buf,4); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint’: ../../src/bigendian.c:299:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 299 | read(fd,buf,4); | ^~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_write_uint8’: ../../src/bigendian.c:367:3: warning: ignoring return value of ‘write’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 367 | write(fd,buf,8); | ^~~~~~~~~~~~~~~ ../../src/bigendian.c: In function ‘Bigendian_fileio_read_uint8’: ../../src/bigendian.c:484:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 484 | read(fd,buf,8); | ^~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univinterval.o `test -f 'univinterval.c' || echo '../../src/'`univinterval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-interval.o `test -f 'interval.c' || echo '../../src/'`interval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stopwatch.o `test -f 'stopwatch.c' || echo '../../src/'`stopwatch.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-semaphore.o `test -f 'semaphore.c' || echo '../../src/'`semaphore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-access.o `test -f 'access.c' || echo '../../src/'`access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-filestring.o `test -f 'filestring.c' || echo '../../src/'`filestring.c ../../src/access.c: In function ‘copy_memory_from_file’: ../../src/access.c:525:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 525 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:530:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fread(p,sizeof(unsigned char),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:536:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 536 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:541:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 541 | fread(p,sizeof(UINT2),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:547:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 547 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:552:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 552 | fread(p,sizeof(UINT4),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:558:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 558 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:563:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 563 | fread(p,sizeof(UINT8),filesize/eltsize - i,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c: In function ‘copy_limited_from_file’: ../../src/access.c:589:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 589 | fread(p,sizeof(unsigned char),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:591:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 591 | fread(p,sizeof(unsigned char),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:597:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 597 | fread(p,sizeof(UINT2),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:599:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 599 | fread(p,sizeof(UINT2),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:605:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 605 | fread(p,sizeof(UINT4),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:607:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 607 | fread(p,sizeof(UINT4),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:613:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 613 | fread(p,sizeof(UINT8),FREAD_BATCH,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/access.c:615:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 615 | fread(p,sizeof(UINT8),filesize/eltsize,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read-univ.o `test -f 'iit-read-univ.c' || echo '../../src/'`iit-read-univ.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-iit-read.o `test -f 'iit-read.c' || echo '../../src/'`iit-read.c In file included from ../../src/iit-read-univ.c:12: ../../src/iit-read-univ.c: In function ‘read_tree_univ’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1068:9: note: in expansion of macro ‘FREAD_UINT’ 1068 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1070:9: note: in expansion of macro ‘FREAD_INT’ 1070 | FREAD_INT(&(new->nodes[i].a),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1071:9: note: in expansion of macro ‘FREAD_INT’ 1071 | FREAD_INT(&(new->nodes[i].b),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1072:9: note: in expansion of macro ‘FREAD_INT’ 1072 | FREAD_INT(&(new->nodes[i].leftindex),fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1073:9: note: in expansion of macro ‘FREAD_INT’ 1073 | FREAD_INT(&(new->nodes[i].rightindex),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_intervals_univ’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1121:7: note: in expansion of macro ‘FREAD_UINT8’ 1121 | FREAD_UINT8(&(new->intervals[i].low),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1122:7: note: in expansion of macro ‘FREAD_UINT8’ 1122 | FREAD_UINT8(&(new->intervals[i].high),fp); | ^~~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1123:7: note: in expansion of macro ‘FREAD_INT’ 1123 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1132:7: note: in expansion of macro ‘FREAD_UINT’ 1132 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1134:7: note: in expansion of macro ‘FREAD_UINT’ 1134 | FREAD_UINT(&uint4,fp); | ^~~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1136:7: note: in expansion of macro ‘FREAD_INT’ 1136 | FREAD_INT(&(new->intervals[i].type),fp); | ^~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1196:3: note: in expansion of macro ‘FREAD_UINT’ 1196 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_annotations’: ../../src/iit-read-univ.c:1389:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1389 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1393:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1393 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1397:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1397 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1401:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1401 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1405:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1405 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c: In function ‘read_words_debug’: ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read-univ.c:1278:3: note: in expansion of macro ‘FREAD_UINT’ 1278 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ In file included from ../../src/iit-read.c:12: ../../src/iit-read.c: In function ‘IIT_read_divint’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2588:5: note: in expansion of macro ‘FREAD_INT’ 2588 | FREAD_INT(&version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_read’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3103:5: note: in expansion of macro ‘FREAD_INT’ 3103 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_tree’: ../../src/iit-read.c:1760:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1760 | fread(&(new->nodes[divno][i].value),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1761:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1761 | fread(&(new->nodes[divno][i].a),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1762:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1762 | fread(&(new->nodes[divno][i].b),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1763:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1763 | fread(&(new->nodes[divno][i].leftindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1764:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1764 | fread(&(new->nodes[divno][i].rightindex),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_intervals’: ../../src/iit-read.c:1889:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1889 | fread(&(new->intervals[divno][i].low),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1890:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1890 | fread(&(new->intervals[divno][i].high),sizeof(unsigned int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1892:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1892 | fread(&(new->intervals[divno][i].sign),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:1896:7: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1896 | fread(&(new->intervals[divno][i].type),sizeof(int),1,fp); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘read_words’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2144:5: note: in expansion of macro ‘FREAD_UINT8’ 2144 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2150:5: note: in expansion of macro ‘FREAD_UINT’ 2150 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ ../../src/iit-read.c: In function ‘read_annotations’: ../../src/iit-read.c:2482:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2482 | read(new->fd,new->valueorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2486:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2486 | read(new->fd,new->values,new->value_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2491:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2491 | read(new->fd,new->labelorder,new->total_nintervals*sizeof(int)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2497:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2497 | read(new->fd,new->labelpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2502:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2502 | read(new->fd,new->labelpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2513:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2513 | read(new->fd,new->labels,new->label_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2519:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2519 | read(new->fd,new->annotpointers8,(new->total_nintervals+1)*sizeof(UINT8)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2524:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2524 | read(new->fd,new->annotpointers,(new->total_nintervals+1)*sizeof(UINT4)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2535:3: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2535 | read(new->fd,new->annotations,new->annot_length*sizeof(char)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c: In function ‘IIT_debug’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:3524:5: note: in expansion of macro ‘FREAD_INT’ 3524 | FREAD_INT(&new->version,fp); | ^~~~~~~~~ ../../src/iit-read.c: In function ‘read_words_debug’: ../../src/littleendian.h:29:27: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 29 | #define FREAD_UINT8(p,fp) fread(p,sizeof(UINT8),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2288:5: note: in expansion of macro ‘FREAD_UINT8’ 2288 | FREAD_UINT8(&length8,fp); | ^~~~~~~~~~~ ../../src/littleendian.h:24:26: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 24 | #define FREAD_UINT(p,fp) fread(p,sizeof(UINT4),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/iit-read.c:2293:5: note: in expansion of macro ‘FREAD_UINT’ 2293 | FREAD_UINT(&length,fp); | ^~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bzip2.o `test -f 'bzip2.c' || echo '../../src/'`bzip2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-reader.o `test -f 'reader.c' || echo '../../src/'`reader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomicpos.o `test -f 'genomicpos.c' || echo '../../src/'`genomicpos.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-compress.o `test -f 'compress.c' || echo '../../src/'`compress.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome.o `test -f 'genome.c' || echo '../../src/'`genome.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome.o `test -f 'transcriptome.c' || echo '../../src/'`transcriptome.c In file included from ../../src/transcriptome.c:29: ../../src/transcriptome.c: In function ‘Transcriptome_new’: ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:159:5: note: in expansion of macro ‘FREAD_INT’ 159 | FREAD_INT(&trnum,fp); | ^~~~~~~~~ ../../src/littleendian.h:23:25: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 23 | #define FREAD_INT(p,fp) fread(p,sizeof(int),1,fp) | ^~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/transcriptome.c:184:5: note: in expansion of macro ‘FREAD_INT’ 184 | FREAD_INT(&divint,fp); | ^~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-popcount.o `test -f 'popcount.c' || echo '../../src/'`popcount.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits.o `test -f 'genomebits.c' || echo '../../src/'`genomebits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_consec.o `test -f 'genomebits_consec.c' || echo '../../src/'`genomebits_consec.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_count.o `test -f 'genomebits_count.c' || echo '../../src/'`genomebits_count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_kmer.o `test -f 'genomebits_kmer.c' || echo '../../src/'`genomebits_kmer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_indel.o `test -f 'genomebits_indel.c' || echo '../../src/'`genomebits_indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_decode.o `test -f 'genomebits_decode.c' || echo '../../src/'`genomebits_decode.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_mismatches.o `test -f 'genomebits_mismatches.c' || echo '../../src/'`genomebits_mismatches.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genomebits_trim.o `test -f 'genomebits_trim.c' || echo '../../src/'`genomebits_trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-dinucl_bits.o `test -f 'dinucl_bits.c' || echo '../../src/'`dinucl_bits.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-genome_sites.o `test -f 'genome_sites.c' || echo '../../src/'`genome_sites.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-read.o `test -f 'bitpack64-read.c' || echo '../../src/'`bitpack64-read.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-readtwo.o `test -f 'bitpack64-readtwo.c' || echo '../../src/'`bitpack64-readtwo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mergeinfo.o `test -f 'mergeinfo.c' || echo '../../src/'`mergeinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint8.o `test -f 'merge-diagonals-heap-uint8.c' || echo '../../src/'`merge-diagonals-heap-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint8.o `test -f 'merge-uint8.c' || echo '../../src/'`merge-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint8.o `test -f 'merge-diagonals-simd-uint8.c' || echo '../../src/'`merge-diagonals-simd-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-heap-uint4.o `test -f 'merge-diagonals-heap-uint4.c' || echo '../../src/'`merge-diagonals-heap-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-uint4.o `test -f 'merge-uint4.c' || echo '../../src/'`merge-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-merge-diagonals-simd-uint4.o `test -f 'merge-diagonals-simd-uint4.c' || echo '../../src/'`merge-diagonals-simd-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indexdb.o `test -f 'indexdb.c' || echo '../../src/'`indexdb.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-localdb-read.o `test -f 'localdb-read.c' || echo '../../src/'`localdb-read.c ../../src/indexdb.c: In function ‘positions_read_multiple_large’: ../../src/indexdb.c:1897:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1897 | read(positions_high_fd,buffer,1); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/indexdb.c:1901:5: warning: ignoring return value of ‘read’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1901 | read(positions_fd,buffer,4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-oligo.o `test -f 'oligo.c' || echo '../../src/'`oligo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-chrnum.o `test -f 'chrnum.c' || echo '../../src/'`chrnum.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-maxent_hr.o `test -f 'maxent_hr.c' || echo '../../src/'`maxent_hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-mapq.o `test -f 'mapq.c' || echo '../../src/'`mapq.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-fopen.o `test -f 'fopen.c' || echo '../../src/'`fopen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-shortread.o `test -f 'shortread.c' || echo '../../src/'`shortread.c In file included from /usr/include/stdio.h:970, from ../../src/shortread.h:8, from ../../src/shortread.c:12: In function ‘fgets’, inlined from ‘input_oneline.constprop’ at ../../src/shortread.c:1145:14: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-junction.o `test -f 'junction.c' || echo '../../src/'`junction.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-concordance.o `test -f 'concordance.c' || echo '../../src/'`concordance.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-simplepair.o `test -f 'simplepair.c' || echo '../../src/'`simplepair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-orderstat.o `test -f 'orderstat.c' || echo '../../src/'`orderstat.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intlistpool.o `test -f 'intlistpool.c' || echo '../../src/'`intlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uintlistpool.o `test -f 'uintlistpool.c' || echo '../../src/'`uintlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8listpool.o `test -f 'uint8listpool.c' || echo '../../src/'`uint8listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-listpool.o `test -f 'listpool.c' || echo '../../src/'`listpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-hitlistpool.o `test -f 'hitlistpool.c' || echo '../../src/'`hitlistpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpool.o `test -f 'pathpool.c' || echo '../../src/'`pathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfopool.o `test -f 'auxinfopool.c' || echo '../../src/'`auxinfopool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstorepool.o `test -f 'pathstorepool.c' || echo '../../src/'`pathstorepool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intron.o `test -f 'intron.c' || echo '../../src/'`intron.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gbuffer.o `test -f 'gbuffer.c' || echo '../../src/'`gbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-common.o `test -f 'select64-common.c' || echo '../../src/'`select64-common.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-ones.o `test -f 'select64-ones.c' || echo '../../src/'`select64-ones.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-select64-zeroes.o `test -f 'select64-zeroes.c' || echo '../../src/'`select64-zeroes.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-ef64.o `test -f 'ef64.c' || echo '../../src/'`ef64.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-nr-x.o `test -f 'nr-x.c' || echo '../../src/'`nr-x.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownsplicing.o `test -f 'knownsplicing.c' || echo '../../src/'`knownsplicing.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-knownindels.o `test -f 'knownindels.c' || echo '../../src/'`knownindels.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice.o `test -f 'splice.c' || echo '../../src/'`splice.c ../../src/knownindels.c: In function ‘Knownindels_new_from_dump’: ../../src/knownindels.c:313:25: warning: format ‘%llu’ expects argument of type ‘long long unsigned int *’, but argument 3 has type ‘Univcoord_T *’ {aka ‘long unsigned int *’} [-Wformat=] 313 | sscanf(line,"%llu %d",&indel_position,&adj) | ~~~^ ~~~~~~~~~~~~~~~ | | | | | Univcoord_T * {aka long unsigned int *} | long long unsigned int * | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-indel.o `test -f 'indel.c' || echo '../../src/'`indel.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceendsgen.o `test -f 'spliceendsgen.c' || echo '../../src/'`spliceendsgen.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-spliceends.o `test -f 'spliceends.c' || echo '../../src/'`spliceends.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitpack64-access.o `test -f 'bitpack64-access.c' || echo '../../src/'`bitpack64-access.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiag.o `test -f 'trdiag.c' || echo '../../src/'`trdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trdiagpool.o `test -f 'trdiagpool.c' || echo '../../src/'`trdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tr-extension-search.o `test -f 'tr-extension-search.c' || echo '../../src/'`tr-extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiag.o `test -f 'univdiag.c' || echo '../../src/'`univdiag.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-univdiagpool.o `test -f 'univdiagpool.c' || echo '../../src/'`univdiagpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-sedgesort.o `test -f 'sedgesort.c' || echo '../../src/'`sedgesort.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-auxinfo.o `test -f 'auxinfo.c' || echo '../../src/'`auxinfo.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathstore.o `test -f 'pathstore.c' || echo '../../src/'`pathstore.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-altsplice.o `test -f 'altsplice.c' || echo '../../src/'`altsplice.c ../../src/altsplice.c: In function ‘Altsplice_print’: ../../src/altsplice.c:124:24: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~^ | | | int | %ld 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/altsplice.c:124:29: warning: format ‘%llu’ expects argument of type ‘long long unsigned int’, but argument 4 has type ‘int’ [-Wformat=] 124 | printf(":%u,len:%d,%llu(%d,%d)", | ~~~^ | | | long long unsigned int | %u 125 | splice_distance,this->univdiagonals[i],distal_length,this->medial_nmismatches,this->distal_nmismatches[i]); | ~~~~~~~~~~~~~ | | | int gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path.o `test -f 'path.c' || echo '../../src/'`path.c ../../src/path.c: In function ‘Path_print’: ../../src/path.c:3321:29: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3321 | printf(">> Path %s %p (%u): ",sensedir_string(this->sensedir),this,this->main_univdiagonal); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/path.c:3336:17: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/path.c:3336:21: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 4 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 3336 | printf("%d[%u..%u]:%s ", | ~^ | | | unsigned int | %lu 3337 | this->chrnum,this->chroffset,this->chrhigh, | ~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair.o `test -f 'pathpair.c' || echo '../../src/'`pathpair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-solve.o `test -f 'path-solve.c' || echo '../../src/'`path-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-fusion.o `test -f 'path-fusion.c' || echo '../../src/'`path-fusion.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-trim.o `test -f 'path-trim.c' || echo '../../src/'`path-trim.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-eval.o `test -f 'path-eval.c' || echo '../../src/'`path-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-pathpair-eval.o `test -f 'pathpair-eval.c' || echo '../../src/'`pathpair-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-alignment.o `test -f 'path-print-alignment.c' || echo '../../src/'`path-print-alignment.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-m8.o `test -f 'path-print-m8.c' || echo '../../src/'`path-print-m8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-print-sam.o `test -f 'path-print-sam.c' || echo '../../src/'`path-print-sam.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-path-learn.o `test -f 'path-learn.c' || echo '../../src/'`path-learn.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-method.o `test -f 'method.c' || echo '../../src/'`method.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-doublelist.o `test -f 'doublelist.c' || echo '../../src/'`doublelist.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-bitvector.o `test -f 'bitvector.c' || echo '../../src/'`bitvector.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptpool.o `test -f 'transcriptpool.c' || echo '../../src/'`transcriptpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-exon.o `test -f 'exon.c' || echo '../../src/'`exon.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript.o `test -f 'transcript.c' || echo '../../src/'`transcript.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpathpool.o `test -f 'trpathpool.c' || echo '../../src/'`trpathpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath.o `test -f 'trpath.c' || echo '../../src/'`trpath.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-solve.o `test -f 'trpath-solve.c' || echo '../../src/'`trpath-solve.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-convert.o `test -f 'trpath-convert.c' || echo '../../src/'`trpath-convert.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-trpath-eval.o `test -f 'trpath-eval.c' || echo '../../src/'`trpath-eval.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcriptome-search.o `test -f 'transcriptome-search.c' || echo '../../src/'`transcriptome-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-vectorpool.o `test -f 'vectorpool.c' || echo '../../src/'`vectorpool.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repair.o `test -f 'repair.c' || echo '../../src/'`repair.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-remap.o `test -f 'transcript-remap.c' || echo '../../src/'`transcript-remap.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-transcript-velocity.o `test -f 'transcript-velocity.c' || echo '../../src/'`transcript-velocity.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-large.o `test -f 'intersect-large.c' || echo '../../src/'`intersect-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-small.o `test -f 'intersect-small.c' || echo '../../src/'`intersect-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-uint2.o `test -f 'intersect-uint2.c' || echo '../../src/'`intersect-uint2.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint4.o `test -f 'intersect-approx-uint4.c' || echo '../../src/'`intersect-approx-uint4.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-uint8.o `test -f 'intersect-approx-uint8.c' || echo '../../src/'`intersect-approx-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-approx-indices-uint8.o `test -f 'intersect-approx-indices-uint8.c' || echo '../../src/'`intersect-approx-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-wdups-indices.o `test -f 'intersect-wdups-indices.c' || echo '../../src/'`intersect-wdups-indices.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-lower-large.o `test -f 'intersect-lower-large.c' || echo '../../src/'`intersect-lower-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-higher-large.o `test -f 'intersect-higher-large.c' || echo '../../src/'`intersect-higher-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-small.o `test -f 'intersect-indices-small.c' || echo '../../src/'`intersect-indices-small.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices2-large.o `test -f 'intersect-indices2-large.c' || echo '../../src/'`intersect-indices2-large.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-indices-uint8.o `test -f 'intersect-indices-uint8.c' || echo '../../src/'`intersect-indices-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-intersect-concordance-uint8.o `test -f 'intersect-concordance-uint8.c' || echo '../../src/'`intersect-concordance-uint8.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-kmer-search.o `test -f 'kmer-search.c' || echo '../../src/'`kmer-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-extension-search.o `test -f 'extension-search.c' || echo '../../src/'`extension-search.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-repetitive.o `test -f 'repetitive.c' || echo '../../src/'`repetitive.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8table.o `test -f 'uint8table.c' || echo '../../src/'`uint8table.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr.o `test -f 'stage1hr.c' || echo '../../src/'`stage1hr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-single.o `test -f 'stage1hr-single.c' || echo '../../src/'`stage1hr-single.c ../../src/stage1hr.c: In function ‘Stage1_list_extension’: ../../src/stage1hr.c:1314:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1314 | printf("%u %d..%d\n",this->extension_gplus[i],this->extension_qstart_gplus[i],this->extension_qend_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1318:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1318 | printf("%u %d..%d\n",this->extension_gminus[i],this->extension_qstart_gminus[i],this->extension_qend_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c: In function ‘Stage1_list_exhaustive’: ../../src/stage1hr.c:1333:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1333 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1334 | this->exhaustive_gplus[i],this->exhaustive_qstart_gplus[i],this->exhaustive_qend_gplus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c:1339:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1339 | printf("%u %d..%d %d\n", | ~^ | | | unsigned int | %lu 1340 | this->exhaustive_gminus[i],this->exhaustive_qstart_gminus[i],this->exhaustive_qend_gminus[i], | ~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | Univcoord_T {aka long unsigned int} ../../src/stage1hr.c: In function ‘Stage1_list_all_univdiagonals’: ../../src/stage1hr.c:1359:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1359 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gplus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu ../../src/stage1hr.c:1394:14: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1394 | printf("%u. Auxinfo methods:",this->all_univdiagonals_gminus[i]); | ~^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | | unsigned int Univcoord_T {aka long unsigned int} | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-stage1hr-paired.o `test -f 'stage1hr-paired.c' || echo '../../src/'`stage1hr-paired.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8tableuint.o `test -f 'uint8tableuint.c' || echo '../../src/'`uint8tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-tableuint.o `test -f 'tableuint.c' || echo '../../src/'`tableuint.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-single-cell.o `test -f 'single-cell.c' || echo '../../src/'`single-cell.c In file included from /usr/include/stdio.h:970, from ../../src/filestring.h:5, from ../../src/single-cell.h:9, from ../../src/single-cell.c:12: In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:404:25, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function ‘fgets’, inlined from ‘input_oneline’ at ../../src/single-cell.c:169:14, inlined from ‘update_whitelist_counts_text’ at ../../src/single-cell.c:412:4, inlined from ‘update_whitelist_counts’ at ../../src/single-cell.c:625:10, inlined from ‘Single_cell_compute_priors’ at ../../src/single-cell.c:728:10: /usr/include/x86_64-linux-gnu/bits/stdio2.h:316:12: warning: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Wattribute-warning] 316 | return __fgets_chk_warn (__s, __sz, __n, __stream); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-request.o `test -f 'request.c' || echo '../../src/'`request.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-resulthr.o `test -f 'resulthr.c' || echo '../../src/'`resulthr.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-output.o `test -f 'output.c' || echo '../../src/'`output.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-inbuffer.o `test -f 'inbuffer.c' || echo '../../src/'`inbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-samheader.o `test -f 'samheader.c' || echo '../../src/'`samheader.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-printbuffer.o `test -f 'printbuffer.c' || echo '../../src/'`printbuffer.c ../../src/samheader.c: In function ‘SAM_header_change_HD_tosorted’: ../../src/samheader.c:236:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 236 | fread(buffer,sizeof(char),CHUNK,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../../src/samheader.c:241:5: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 241 | fread(buffer,sizeof(char),headerlen,input); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-outbuffer.o `test -f 'outbuffer.c' || echo '../../src/'`outbuffer.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-uint8pairtable.o `test -f 'uint8pairtable.c' || echo '../../src/'`uint8pairtable.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-splice-count.o `test -f 'splice-count.c' || echo '../../src/'`splice-count.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-support.o `test -f 'support.c' || echo '../../src/'`support.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-datadir.o `test -f 'datadir.c' || echo '../../src/'`datadir.c ../../src/support.c: In function ‘Support_dump’: ../../src/support.c:950:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 950 | fprintf(fp,"%u\t",donor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:951:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 951 | fprintf(fp,"%u\t",acceptor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1021:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1021 | fprintf(fp,"%u\t",acceptor_position - chroffset + INTRON_ADJ); /* low position */ | ~^ | | | unsigned int | %lu ../../src/support.c:1022:20: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 3 has type ‘Univcoord_T’ {aka ‘long unsigned int’} [-Wformat=] 1022 | fprintf(fp,"%u\t",donor_position - chroffset + 1 - INTRON_ADJ); /* high position */ | ~^ | | | unsigned int | %lu gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-parserange.o `test -f 'parserange.c' || echo '../../src/'`parserange.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-getline.o `test -f 'getline.c' || echo '../../src/'`getline.c gcc -DHAVE_CONFIG_H -I. -I../../src -Wdate-time -D_FORTIFY_SOURCE=2 -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -c -o gsnapl_avx512-gsnap.o `test -f 'gsnap.c' || echo '../../src/'`gsnap.c gcc -DMAIN=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cpuid cpuid-cpuid.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap gmap-cpuid.o gmap-gmap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl gmapl-cpuid.o gmapl-gmapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o get-genome get_genome-except.o get_genome-assert.o get_genome-mem.o get_genome-intlist.o get_genome-list.o get_genome-littleendian.o get_genome-bigendian.o get_genome-univinterval.o get_genome-interval.o get_genome-uintlist.o get_genome-stopwatch.o get_genome-semaphore.o get_genome-access.o get_genome-filestring.o get_genome-iit-read-univ.o get_genome-iit-read.o get_genome-md5.o get_genome-bzip2.o get_genome-fopen.o get_genome-sequence.o get_genome-genome.o get_genome-genomicpos.o get_genome-chrom.o get_genome-chrnum.o get_genome-datadir.o get_genome-parserange.o get_genome-getline.o get_genome-get-genome.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapindex gmapindex-except.o gmapindex-assert.o gmapindex-mem.o gmapindex-intlist.o gmapindex-list.o gmapindex-littleendian.o gmapindex-bigendian.o gmapindex-univinterval.o gmapindex-interval.o gmapindex-uintlist.o gmapindex-stopwatch.o gmapindex-semaphore.o gmapindex-access.o gmapindex-filestring.o gmapindex-iit-read-univ.o gmapindex-iit-write-univ.o gmapindex-iit-read.o gmapindex-md5.o gmapindex-bzip2.o gmapindex-fopen.o gmapindex-sequence.o gmapindex-genome.o gmapindex-genomicpos.o gmapindex-compress-write.o gmapindex-genome-write.o gmapindex-compress.o gmapindex-popcount.o gmapindex-bitpack64-read.o gmapindex-bitpack64-readtwo.o gmapindex-bitpack64-access.o gmapindex-bitpack64-incr.o gmapindex-bitpack64-write.o gmapindex-indexdb.o gmapindex-indexdb-write.o gmapindex-saca-k.o gmapindex-localdb-write.o gmapindex-table.o gmapindex-tableuint.o gmapindex-tableuint8.o gmapindex-tableint.o gmapindex-bytecoding.o gmapindex-sarray-write.o gmapindex-chrom.o gmapindex-segmentpos.o gmapindex-uint8list.o gmapindex-parserange.o gmapindex-getline.o gmapindex-gmapindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o indexdb_cat indexdb_cat-except.o indexdb_cat-assert.o indexdb_cat-mem.o indexdb_cat-littleendian.o indexdb_cat-bigendian.o indexdb_cat-genomicpos.o indexdb_cat-stopwatch.o indexdb_cat-semaphore.o indexdb_cat-access.o indexdb_cat-univinterval.o indexdb_cat-interval.o indexdb_cat-uintlist.o indexdb_cat-intlist.o indexdb_cat-list.o indexdb_cat-filestring.o indexdb_cat-iit-read-univ.o indexdb_cat-iit-read.o indexdb_cat-popcount.o indexdb_cat-bitpack64-read.o indexdb_cat-bitpack64-readtwo.o indexdb_cat-bitpack64-access.o indexdb_cat-bitpack64-incr.o indexdb_cat-bitpack64-write.o indexdb_cat-indexdb.o indexdb_cat-indexdb-write.o indexdb_cat-compress-write.o indexdb_cat-bzip2.o indexdb_cat-fopen.o indexdb_cat-datadir.o indexdb_cat-parserange.o indexdb_cat-getline.o indexdb_cat-indexdb-cat.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_store iit_store-except.o iit_store-assert.o iit_store-mem.o iit_store-intlist.o iit_store-list.o iit_store-littleendian.o iit_store-bigendian.o iit_store-univinterval.o iit_store-interval.o iit_store-uintlist.o iit_store-stopwatch.o iit_store-semaphore.o iit_store-access.o iit_store-doublelist.o iit_store-iit-write-univ.o iit_store-iit-write.o iit_store-tableint.o iit_store-table.o iit_store-chrom.o iit_store-bzip2.o iit_store-getline.o iit_store-iit_store.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_get iit_get-except.o iit_get-assert.o iit_get-mem.o iit_get-intlist.o iit_get-list.o iit_get-littleendian.o iit_get-bigendian.o iit_get-univinterval.o iit_get-interval.o iit_get-uintlist.o iit_get-stopwatch.o iit_get-semaphore.o iit_get-access.o iit_get-filestring.o iit_get-iit-read-univ.o iit_get-iit-read.o iit_get-parserange.o iit_get-bzip2.o iit_get-getline.o iit_get-iit_get.o -lz -lbz2 -lm gcc -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o iit_dump iit_dump-except.o iit_dump-assert.o iit_dump-mem.o iit_dump-littleendian.o iit_dump-bigendian.o iit_dump-intlist.o iit_dump-list.o iit_dump-univinterval.o iit_dump-interval.o iit_dump-uintlist.o iit_dump-stopwatch.o iit_dump-semaphore.o iit_dump-access.o iit_dump-filestring.o iit_dump-iit-read-univ.o iit_dump-iit-read.o iit_dump-parserange.o iit_dump-iit_dump.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap gsnap-cpuid.o gsnap-gsnap_select.o -lm gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl gsnapl-cpuid.o gsnapl-gsnapl_select.o -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o snpindex snpindex-except.o snpindex-assert.o snpindex-mem.o snpindex-intlist.o snpindex-list.o snpindex-littleendian.o snpindex-bigendian.o snpindex-univinterval.o snpindex-interval.o snpindex-uintlist.o snpindex-stopwatch.o snpindex-semaphore.o snpindex-access.o snpindex-filestring.o snpindex-iit-read-univ.o snpindex-iit-read.o snpindex-genomicpos.o snpindex-compress.o snpindex-compress-write.o snpindex-popcount.o snpindex-bitpack64-read.o snpindex-bitpack64-readtwo.o snpindex-bitpack64-access.o snpindex-bitpack64-incr.o snpindex-bitpack64-write.o snpindex-indexdb.o snpindex-indexdb-write.o snpindex-chrom.o snpindex-md5.o snpindex-bzip2.o snpindex-fopen.o snpindex-sequence.o snpindex-genome.o snpindex-datadir.o snpindex-parserange.o snpindex-getline.o snpindex-snpindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o cmetindex cmetindex-except.o cmetindex-assert.o cmetindex-mem.o cmetindex-littleendian.o cmetindex-bigendian.o cmetindex-genomicpos.o cmetindex-stopwatch.o cmetindex-semaphore.o cmetindex-access.o cmetindex-univinterval.o cmetindex-interval.o cmetindex-filestring.o cmetindex-iit-read-univ.o cmetindex-iit-read.o cmetindex-compress.o cmetindex-compress-write.o cmetindex-popcount.o cmetindex-bitpack64-read.o cmetindex-bitpack64-readtwo.o cmetindex-bitpack64-access.o cmetindex-bitpack64-incr.o cmetindex-bitpack64-write.o cmetindex-indexdb.o cmetindex-indexdb-write.o cmetindex-cmet.o cmetindex-md5.o cmetindex-bzip2.o cmetindex-fopen.o cmetindex-sequence.o cmetindex-genome.o cmetindex-uintlist.o cmetindex-intlist.o cmetindex-uint8list.o cmetindex-list.o cmetindex-datadir.o cmetindex-parserange.o cmetindex-getline.o cmetindex-cmetindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o atoiindex atoiindex-except.o atoiindex-assert.o atoiindex-mem.o atoiindex-littleendian.o atoiindex-bigendian.o atoiindex-genomicpos.o atoiindex-stopwatch.o atoiindex-semaphore.o atoiindex-access.o atoiindex-univinterval.o atoiindex-interval.o atoiindex-filestring.o atoiindex-iit-read-univ.o atoiindex-iit-read.o atoiindex-compress.o atoiindex-compress-write.o atoiindex-popcount.o atoiindex-bitpack64-read.o atoiindex-bitpack64-readtwo.o atoiindex-bitpack64-access.o atoiindex-bitpack64-incr.o atoiindex-bitpack64-write.o atoiindex-indexdb.o atoiindex-indexdb-write.o atoiindex-atoi.o atoiindex-md5.o atoiindex-bzip2.o atoiindex-fopen.o atoiindex-sequence.o atoiindex-genome.o atoiindex-uintlist.o atoiindex-intlist.o atoiindex-uint8list.o atoiindex-list.o atoiindex-datadir.o atoiindex-parserange.o atoiindex-getline.o atoiindex-atoiindex.o -lz -lbz2 -lm gcc -DGMAPDB=\"/var/cache/gmap\" -DUTILITYP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o trindex trindex-except.o trindex-assert.o trindex-mem.o trindex-littleendian.o trindex-bigendian.o trindex-genomicpos.o trindex-stopwatch.o trindex-semaphore.o trindex-access.o trindex-interval.o trindex-filestring.o trindex-iit-read.o trindex-parserange.o trindex-univinterval.o trindex-iit-read-univ.o trindex-popcount.o trindex-bitpack64-access.o trindex-bitpack64-write.o trindex-uintlist.o trindex-intlist.o trindex-list.o trindex-bitpack64-readtwo.o trindex-transcriptome.o trindex-datadir.o trindex-bzip2.o trindex-getline.o trindex-trindex.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.nosimd gmap_nosimd-except.o gmap_nosimd-assert.o gmap_nosimd-mem.o gmap_nosimd-intlist.o gmap_nosimd-uintlist.o gmap_nosimd-list.o gmap_nosimd-littleendian.o gmap_nosimd-bigendian.o gmap_nosimd-univinterval.o gmap_nosimd-interval.o gmap_nosimd-stopwatch.o gmap_nosimd-semaphore.o gmap_nosimd-access.o gmap_nosimd-filestring.o gmap_nosimd-iit-read-univ.o gmap_nosimd-iit-read.o gmap_nosimd-md5.o gmap_nosimd-bzip2.o gmap_nosimd-fopen.o gmap_nosimd-sequence.o gmap_nosimd-reader.o gmap_nosimd-genomicpos.o gmap_nosimd-compress.o gmap_nosimd-compress-write.o gmap_nosimd-gbuffer.o gmap_nosimd-genome.o gmap_nosimd-popcount.o gmap_nosimd-dinucl_bits.o gmap_nosimd-genome_canonical.o gmap_nosimd-genome-write.o gmap_nosimd-bitpack64-read.o gmap_nosimd-bitpack64-readtwo.o gmap_nosimd-indexdb.o gmap_nosimd-oligo.o gmap_nosimd-block.o gmap_nosimd-chrom.o gmap_nosimd-segmentpos.o gmap_nosimd-chrnum.o gmap_nosimd-uinttable_rh.o gmap_nosimd-gregion.o gmap_nosimd-match.o gmap_nosimd-matchpool.o gmap_nosimd-diagnostic.o gmap_nosimd-stage1.o gmap_nosimd-diag.o gmap_nosimd-diagpool.o gmap_nosimd-cmet.o gmap_nosimd-atoi.o gmap_nosimd-orderstat.o gmap_nosimd-oligoindex_hr.o gmap_nosimd-intron.o gmap_nosimd-maxent.o gmap_nosimd-maxent_hr.o gmap_nosimd-pair.o gmap_nosimd-pairpool.o gmap_nosimd-cellpool.o gmap_nosimd-stage2.o gmap_nosimd-doublelist.o gmap_nosimd-smooth.o gmap_nosimd-splicestringpool.o gmap_nosimd-splicetrie_build.o gmap_nosimd-splicetrie.o gmap_nosimd-boyer-moore.o gmap_nosimd-dynprog.o gmap_nosimd-dynprog_simd.o gmap_nosimd-dynprog_single.o gmap_nosimd-dynprog_genome.o gmap_nosimd-dynprog_cdna.o gmap_nosimd-dynprog_end.o gmap_nosimd-translation.o gmap_nosimd-pbinom.o gmap_nosimd-changepoint.o gmap_nosimd-stage3.o gmap_nosimd-request.o gmap_nosimd-result.o gmap_nosimd-output.o gmap_nosimd-inbuffer.o gmap_nosimd-samheader.o gmap_nosimd-printbuffer.o gmap_nosimd-outbuffer.o gmap_nosimd-chimera.o gmap_nosimd-datadir.o gmap_nosimd-parserange.o gmap_nosimd-getline.o gmap_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.nosimd gmapl_nosimd-except.o gmapl_nosimd-assert.o gmapl_nosimd-mem.o gmapl_nosimd-intlist.o gmapl_nosimd-uintlist.o gmapl_nosimd-uint8list.o gmapl_nosimd-list.o gmapl_nosimd-littleendian.o gmapl_nosimd-bigendian.o gmapl_nosimd-univinterval.o gmapl_nosimd-interval.o gmapl_nosimd-stopwatch.o gmapl_nosimd-semaphore.o gmapl_nosimd-access.o gmapl_nosimd-filestring.o gmapl_nosimd-iit-read-univ.o gmapl_nosimd-iit-read.o gmapl_nosimd-md5.o gmapl_nosimd-bzip2.o gmapl_nosimd-fopen.o gmapl_nosimd-sequence.o gmapl_nosimd-reader.o gmapl_nosimd-genomicpos.o gmapl_nosimd-compress.o gmapl_nosimd-compress-write.o gmapl_nosimd-gbuffer.o gmapl_nosimd-genome.o gmapl_nosimd-popcount.o gmapl_nosimd-dinucl_bits.o gmapl_nosimd-genome_canonical.o gmapl_nosimd-genome-write.o gmapl_nosimd-bitpack64-read.o gmapl_nosimd-bitpack64-readtwo.o gmapl_nosimd-indexdb.o gmapl_nosimd-oligo.o gmapl_nosimd-block.o gmapl_nosimd-chrom.o gmapl_nosimd-segmentpos.o gmapl_nosimd-chrnum.o gmapl_nosimd-uinttable_rh.o gmapl_nosimd-uint8table_rh.o gmapl_nosimd-gregion.o gmapl_nosimd-match.o gmapl_nosimd-matchpool.o gmapl_nosimd-diagnostic.o gmapl_nosimd-stage1.o gmapl_nosimd-diag.o gmapl_nosimd-diagpool.o gmapl_nosimd-cmet.o gmapl_nosimd-atoi.o gmapl_nosimd-orderstat.o gmapl_nosimd-oligoindex_hr.o gmapl_nosimd-intron.o gmapl_nosimd-maxent.o gmapl_nosimd-maxent_hr.o gmapl_nosimd-pair.o gmapl_nosimd-pairpool.o gmapl_nosimd-cellpool.o gmapl_nosimd-stage2.o gmapl_nosimd-doublelist.o gmapl_nosimd-smooth.o gmapl_nosimd-splicestringpool.o gmapl_nosimd-splicetrie_build.o gmapl_nosimd-splicetrie.o gmapl_nosimd-boyer-moore.o gmapl_nosimd-dynprog.o gmapl_nosimd-dynprog_simd.o gmapl_nosimd-dynprog_single.o gmapl_nosimd-dynprog_genome.o gmapl_nosimd-dynprog_cdna.o gmapl_nosimd-dynprog_end.o gmapl_nosimd-translation.o gmapl_nosimd-pbinom.o gmapl_nosimd-changepoint.o gmapl_nosimd-stage3.o gmapl_nosimd-request.o gmapl_nosimd-result.o gmapl_nosimd-output.o gmapl_nosimd-inbuffer.o gmapl_nosimd-samheader.o gmapl_nosimd-printbuffer.o gmapl_nosimd-outbuffer.o gmapl_nosimd-chimera.o gmapl_nosimd-datadir.o gmapl_nosimd-parserange.o gmapl_nosimd-getline.o gmapl_nosimd-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.nosimd gsnap_nosimd-except.o gsnap_nosimd-assert.o gsnap_nosimd-mem.o gsnap_nosimd-intlist.o gsnap_nosimd-uintlist.o gsnap_nosimd-list.o gsnap_nosimd-littleendian.o gsnap_nosimd-bigendian.o gsnap_nosimd-univinterval.o gsnap_nosimd-interval.o gsnap_nosimd-stopwatch.o gsnap_nosimd-semaphore.o gsnap_nosimd-access.o gsnap_nosimd-filestring.o gsnap_nosimd-iit-read-univ.o gsnap_nosimd-iit-read.o gsnap_nosimd-bzip2.o gsnap_nosimd-reader.o gsnap_nosimd-genomicpos.o gsnap_nosimd-compress.o gsnap_nosimd-genome.o gsnap_nosimd-transcriptome.o gsnap_nosimd-popcount.o gsnap_nosimd-genomebits.o gsnap_nosimd-genomebits_consec.o gsnap_nosimd-genomebits_count.o gsnap_nosimd-genomebits_kmer.o gsnap_nosimd-genomebits_indel.o gsnap_nosimd-genomebits_decode.o gsnap_nosimd-genomebits_mismatches.o gsnap_nosimd-genomebits_trim.o gsnap_nosimd-dinucl_bits.o gsnap_nosimd-genome_sites.o gsnap_nosimd-bitpack64-read.o gsnap_nosimd-bitpack64-readtwo.o gsnap_nosimd-mergeinfo.o gsnap_nosimd-merge-diagonals-heap-uint4.o gsnap_nosimd-merge-uint4.o gsnap_nosimd-merge-diagonals-simd-uint4.o gsnap_nosimd-indexdb.o gsnap_nosimd-localdb-read.o gsnap_nosimd-oligo.o gsnap_nosimd-chrnum.o gsnap_nosimd-maxent_hr.o gsnap_nosimd-mapq.o gsnap_nosimd-fopen.o gsnap_nosimd-shortread.o gsnap_nosimd-junction.o gsnap_nosimd-concordance.o gsnap_nosimd-simplepair.o gsnap_nosimd-orderstat.o gsnap_nosimd-intlistpool.o gsnap_nosimd-uintlistpool.o gsnap_nosimd-listpool.o gsnap_nosimd-hitlistpool.o gsnap_nosimd-pathpool.o gsnap_nosimd-auxinfopool.o gsnap_nosimd-pathstorepool.o gsnap_nosimd-intron.o gsnap_nosimd-gbuffer.o gsnap_nosimd-select64-common.o gsnap_nosimd-select64-ones.o gsnap_nosimd-select64-zeroes.o gsnap_nosimd-ef64.o gsnap_nosimd-nr-x.o gsnap_nosimd-knownsplicing.o gsnap_nosimd-knownindels.o gsnap_nosimd-splice.o gsnap_nosimd-indel.o gsnap_nosimd-spliceendsgen.o gsnap_nosimd-spliceends.o gsnap_nosimd-bitpack64-access.o gsnap_nosimd-trdiag.o gsnap_nosimd-trdiagpool.o gsnap_nosimd-tr-extension-search.o gsnap_nosimd-univdiag.o gsnap_nosimd-univdiagpool.o gsnap_nosimd-sedgesort.o gsnap_nosimd-auxinfo.o gsnap_nosimd-pathstore.o gsnap_nosimd-altsplice.o gsnap_nosimd-path.o gsnap_nosimd-pathpair.o gsnap_nosimd-path-solve.o gsnap_nosimd-path-fusion.o gsnap_nosimd-path-trim.o gsnap_nosimd-path-eval.o gsnap_nosimd-pathpair-eval.o gsnap_nosimd-path-print-alignment.o gsnap_nosimd-path-print-m8.o gsnap_nosimd-path-print-sam.o gsnap_nosimd-path-learn.o gsnap_nosimd-method.o gsnap_nosimd-doublelist.o gsnap_nosimd-bitvector.o gsnap_nosimd-transcriptpool.o gsnap_nosimd-exon.o gsnap_nosimd-transcript.o gsnap_nosimd-trpathpool.o gsnap_nosimd-trpath.o gsnap_nosimd-trpath-solve.o gsnap_nosimd-trpath-convert.o gsnap_nosimd-trpath-eval.o gsnap_nosimd-transcriptome-search.o gsnap_nosimd-vectorpool.o gsnap_nosimd-repair.o gsnap_nosimd-transcript-remap.o gsnap_nosimd-transcript-velocity.o gsnap_nosimd-intersect-small.o gsnap_nosimd-intersect-uint2.o gsnap_nosimd-intersect-approx-uint4.o gsnap_nosimd-intersect-approx-indices-uint4.o gsnap_nosimd-intersect-wdups-indices.o gsnap_nosimd-intersect-lower-small.o gsnap_nosimd-intersect-higher-small.o gsnap_nosimd-intersect-indices-small.o gsnap_nosimd-intersect-indices2-small.o gsnap_nosimd-intersect-concordance-uint4.o gsnap_nosimd-kmer-search.o gsnap_nosimd-extension-search.o gsnap_nosimd-repetitive.o gsnap_nosimd-uint8table.o gsnap_nosimd-uinttable.o gsnap_nosimd-stage1hr.o gsnap_nosimd-stage1hr-single.o gsnap_nosimd-stage1hr-paired.o gsnap_nosimd-uinttableuint.o gsnap_nosimd-tableuint.o gsnap_nosimd-single-cell.o gsnap_nosimd-request.o gsnap_nosimd-resulthr.o gsnap_nosimd-output.o gsnap_nosimd-inbuffer.o gsnap_nosimd-samheader.o gsnap_nosimd-printbuffer.o gsnap_nosimd-outbuffer.o gsnap_nosimd-uintpairtable.o gsnap_nosimd-splice-count.o gsnap_nosimd-support.o gsnap_nosimd-datadir.o gsnap_nosimd-parserange.o gsnap_nosimd-getline.o gsnap_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.nosimd gsnapl_nosimd-except.o gsnapl_nosimd-assert.o gsnapl_nosimd-mem.o gsnapl_nosimd-intlist.o gsnapl_nosimd-uintlist.o gsnapl_nosimd-uint8list.o gsnapl_nosimd-list.o gsnapl_nosimd-littleendian.o gsnapl_nosimd-bigendian.o gsnapl_nosimd-univinterval.o gsnapl_nosimd-interval.o gsnapl_nosimd-stopwatch.o gsnapl_nosimd-semaphore.o gsnapl_nosimd-access.o gsnapl_nosimd-filestring.o gsnapl_nosimd-iit-read-univ.o gsnapl_nosimd-iit-read.o gsnapl_nosimd-bzip2.o gsnapl_nosimd-reader.o gsnapl_nosimd-genomicpos.o gsnapl_nosimd-compress.o gsnapl_nosimd-genome.o gsnapl_nosimd-transcriptome.o gsnapl_nosimd-popcount.o gsnapl_nosimd-genomebits.o gsnapl_nosimd-genomebits_consec.o gsnapl_nosimd-genomebits_count.o gsnapl_nosimd-genomebits_kmer.o gsnapl_nosimd-genomebits_indel.o gsnapl_nosimd-genomebits_decode.o gsnapl_nosimd-genomebits_mismatches.o gsnapl_nosimd-genomebits_trim.o gsnapl_nosimd-dinucl_bits.o gsnapl_nosimd-genome_sites.o gsnapl_nosimd-bitpack64-read.o gsnapl_nosimd-bitpack64-readtwo.o gsnapl_nosimd-mergeinfo.o gsnapl_nosimd-merge-diagonals-heap-uint8.o gsnapl_nosimd-merge-uint8.o gsnapl_nosimd-merge-diagonals-simd-uint8.o gsnapl_nosimd-merge-diagonals-heap-uint4.o gsnapl_nosimd-merge-uint4.o gsnapl_nosimd-merge-diagonals-simd-uint4.o gsnapl_nosimd-indexdb.o gsnapl_nosimd-localdb-read.o gsnapl_nosimd-oligo.o gsnapl_nosimd-chrnum.o gsnapl_nosimd-maxent_hr.o gsnapl_nosimd-mapq.o gsnapl_nosimd-fopen.o gsnapl_nosimd-shortread.o gsnapl_nosimd-junction.o gsnapl_nosimd-concordance.o gsnapl_nosimd-simplepair.o gsnapl_nosimd-orderstat.o gsnapl_nosimd-intlistpool.o gsnapl_nosimd-uintlistpool.o gsnapl_nosimd-uint8listpool.o gsnapl_nosimd-listpool.o gsnapl_nosimd-hitlistpool.o gsnapl_nosimd-pathpool.o gsnapl_nosimd-auxinfopool.o gsnapl_nosimd-pathstorepool.o gsnapl_nosimd-intron.o gsnapl_nosimd-gbuffer.o gsnapl_nosimd-select64-common.o gsnapl_nosimd-select64-ones.o gsnapl_nosimd-select64-zeroes.o gsnapl_nosimd-ef64.o gsnapl_nosimd-nr-x.o gsnapl_nosimd-knownsplicing.o gsnapl_nosimd-knownindels.o gsnapl_nosimd-splice.o gsnapl_nosimd-indel.o gsnapl_nosimd-spliceendsgen.o gsnapl_nosimd-spliceends.o gsnapl_nosimd-bitpack64-access.o gsnapl_nosimd-trdiag.o gsnapl_nosimd-trdiagpool.o gsnapl_nosimd-tr-extension-search.o gsnapl_nosimd-univdiag.o gsnapl_nosimd-univdiagpool.o gsnapl_nosimd-sedgesort.o gsnapl_nosimd-auxinfo.o gsnapl_nosimd-pathstore.o gsnapl_nosimd-altsplice.o gsnapl_nosimd-path.o gsnapl_nosimd-pathpair.o gsnapl_nosimd-path-solve.o gsnapl_nosimd-path-fusion.o gsnapl_nosimd-path-trim.o gsnapl_nosimd-path-eval.o gsnapl_nosimd-pathpair-eval.o gsnapl_nosimd-path-print-alignment.o gsnapl_nosimd-path-print-m8.o gsnapl_nosimd-path-print-sam.o gsnapl_nosimd-path-learn.o gsnapl_nosimd-method.o gsnapl_nosimd-doublelist.o gsnapl_nosimd-bitvector.o gsnapl_nosimd-transcriptpool.o gsnapl_nosimd-exon.o gsnapl_nosimd-transcript.o gsnapl_nosimd-trpathpool.o gsnapl_nosimd-trpath.o gsnapl_nosimd-trpath-solve.o gsnapl_nosimd-trpath-convert.o gsnapl_nosimd-trpath-eval.o gsnapl_nosimd-transcriptome-search.o gsnapl_nosimd-vectorpool.o gsnapl_nosimd-repair.o gsnapl_nosimd-transcript-remap.o gsnapl_nosimd-transcript-velocity.o gsnapl_nosimd-intersect-large.o gsnapl_nosimd-intersect-small.o gsnapl_nosimd-intersect-uint2.o gsnapl_nosimd-intersect-approx-uint4.o gsnapl_nosimd-intersect-approx-uint8.o gsnapl_nosimd-intersect-approx-indices-uint8.o gsnapl_nosimd-intersect-wdups-indices.o gsnapl_nosimd-intersect-lower-large.o gsnapl_nosimd-intersect-higher-large.o gsnapl_nosimd-intersect-indices-small.o gsnapl_nosimd-intersect-indices2-large.o gsnapl_nosimd-intersect-indices-uint8.o gsnapl_nosimd-intersect-concordance-uint8.o gsnapl_nosimd-kmer-search.o gsnapl_nosimd-extension-search.o gsnapl_nosimd-repetitive.o gsnapl_nosimd-uint8table.o gsnapl_nosimd-stage1hr.o gsnapl_nosimd-stage1hr-single.o gsnapl_nosimd-stage1hr-paired.o gsnapl_nosimd-uint8tableuint.o gsnapl_nosimd-tableuint.o gsnapl_nosimd-single-cell.o gsnapl_nosimd-request.o gsnapl_nosimd-resulthr.o gsnapl_nosimd-output.o gsnapl_nosimd-inbuffer.o gsnapl_nosimd-samheader.o gsnapl_nosimd-printbuffer.o gsnapl_nosimd-outbuffer.o gsnapl_nosimd-uint8pairtable.o gsnapl_nosimd-splice-count.o gsnapl_nosimd-support.o gsnapl_nosimd-datadir.o gsnapl_nosimd-parserange.o gsnapl_nosimd-getline.o gsnapl_nosimd-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmap.avx512 gmap_avx512-except.o gmap_avx512-assert.o gmap_avx512-mem.o gmap_avx512-intlist.o gmap_avx512-uintlist.o gmap_avx512-list.o gmap_avx512-littleendian.o gmap_avx512-bigendian.o gmap_avx512-univinterval.o gmap_avx512-interval.o gmap_avx512-stopwatch.o gmap_avx512-semaphore.o gmap_avx512-access.o gmap_avx512-filestring.o gmap_avx512-iit-read-univ.o gmap_avx512-iit-read.o gmap_avx512-md5.o gmap_avx512-bzip2.o gmap_avx512-fopen.o gmap_avx512-sequence.o gmap_avx512-reader.o gmap_avx512-genomicpos.o gmap_avx512-compress.o gmap_avx512-compress-write.o gmap_avx512-gbuffer.o gmap_avx512-genome.o gmap_avx512-popcount.o gmap_avx512-dinucl_bits.o gmap_avx512-genome_canonical.o gmap_avx512-genome-write.o gmap_avx512-bitpack64-read.o gmap_avx512-bitpack64-readtwo.o gmap_avx512-indexdb.o gmap_avx512-oligo.o gmap_avx512-block.o gmap_avx512-chrom.o gmap_avx512-segmentpos.o gmap_avx512-chrnum.o gmap_avx512-uinttable_rh.o gmap_avx512-gregion.o gmap_avx512-match.o gmap_avx512-matchpool.o gmap_avx512-diagnostic.o gmap_avx512-stage1.o gmap_avx512-diag.o gmap_avx512-diagpool.o gmap_avx512-cmet.o gmap_avx512-atoi.o gmap_avx512-orderstat.o gmap_avx512-oligoindex_hr.o gmap_avx512-intron.o gmap_avx512-maxent.o gmap_avx512-maxent_hr.o gmap_avx512-pair.o gmap_avx512-pairpool.o gmap_avx512-cellpool.o gmap_avx512-stage2.o gmap_avx512-doublelist.o gmap_avx512-smooth.o gmap_avx512-splicestringpool.o gmap_avx512-splicetrie_build.o gmap_avx512-splicetrie.o gmap_avx512-boyer-moore.o gmap_avx512-dynprog.o gmap_avx512-dynprog_simd.o gmap_avx512-dynprog_single.o gmap_avx512-dynprog_genome.o gmap_avx512-dynprog_cdna.o gmap_avx512-dynprog_end.o gmap_avx512-translation.o gmap_avx512-pbinom.o gmap_avx512-changepoint.o gmap_avx512-stage3.o gmap_avx512-request.o gmap_avx512-result.o gmap_avx512-output.o gmap_avx512-inbuffer.o gmap_avx512-samheader.o gmap_avx512-printbuffer.o gmap_avx512-outbuffer.o gmap_avx512-chimera.o gmap_avx512-datadir.o gmap_avx512-parserange.o gmap_avx512-getline.o gmap_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gmapl.avx512 gmapl_avx512-except.o gmapl_avx512-assert.o gmapl_avx512-mem.o gmapl_avx512-intlist.o gmapl_avx512-uintlist.o gmapl_avx512-uint8list.o gmapl_avx512-list.o gmapl_avx512-littleendian.o gmapl_avx512-bigendian.o gmapl_avx512-univinterval.o gmapl_avx512-interval.o gmapl_avx512-stopwatch.o gmapl_avx512-semaphore.o gmapl_avx512-access.o gmapl_avx512-filestring.o gmapl_avx512-iit-read-univ.o gmapl_avx512-iit-read.o gmapl_avx512-md5.o gmapl_avx512-bzip2.o gmapl_avx512-fopen.o gmapl_avx512-sequence.o gmapl_avx512-reader.o gmapl_avx512-genomicpos.o gmapl_avx512-compress.o gmapl_avx512-compress-write.o gmapl_avx512-gbuffer.o gmapl_avx512-genome.o gmapl_avx512-popcount.o gmapl_avx512-dinucl_bits.o gmapl_avx512-genome_canonical.o gmapl_avx512-genome-write.o gmapl_avx512-bitpack64-read.o gmapl_avx512-bitpack64-readtwo.o gmapl_avx512-indexdb.o gmapl_avx512-oligo.o gmapl_avx512-block.o gmapl_avx512-chrom.o gmapl_avx512-segmentpos.o gmapl_avx512-chrnum.o gmapl_avx512-uinttable_rh.o gmapl_avx512-uint8table_rh.o gmapl_avx512-gregion.o gmapl_avx512-match.o gmapl_avx512-matchpool.o gmapl_avx512-diagnostic.o gmapl_avx512-stage1.o gmapl_avx512-diag.o gmapl_avx512-diagpool.o gmapl_avx512-cmet.o gmapl_avx512-atoi.o gmapl_avx512-orderstat.o gmapl_avx512-oligoindex_hr.o gmapl_avx512-intron.o gmapl_avx512-maxent.o gmapl_avx512-maxent_hr.o gmapl_avx512-pair.o gmapl_avx512-pairpool.o gmapl_avx512-cellpool.o gmapl_avx512-stage2.o gmapl_avx512-doublelist.o gmapl_avx512-smooth.o gmapl_avx512-splicestringpool.o gmapl_avx512-splicetrie_build.o gmapl_avx512-splicetrie.o gmapl_avx512-boyer-moore.o gmapl_avx512-dynprog.o gmapl_avx512-dynprog_simd.o gmapl_avx512-dynprog_single.o gmapl_avx512-dynprog_genome.o gmapl_avx512-dynprog_cdna.o gmapl_avx512-dynprog_end.o gmapl_avx512-translation.o gmapl_avx512-pbinom.o gmapl_avx512-changepoint.o gmapl_avx512-stage3.o gmapl_avx512-request.o gmapl_avx512-result.o gmapl_avx512-output.o gmapl_avx512-inbuffer.o gmapl_avx512-samheader.o gmapl_avx512-printbuffer.o gmapl_avx512-outbuffer.o gmapl_avx512-chimera.o gmapl_avx512-datadir.o gmapl_avx512-parserange.o gmapl_avx512-getline.o gmapl_avx512-gmap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnap.avx512 gsnap_avx512-except.o gsnap_avx512-assert.o gsnap_avx512-mem.o gsnap_avx512-intlist.o gsnap_avx512-uintlist.o gsnap_avx512-list.o gsnap_avx512-littleendian.o gsnap_avx512-bigendian.o gsnap_avx512-univinterval.o gsnap_avx512-interval.o gsnap_avx512-stopwatch.o gsnap_avx512-semaphore.o gsnap_avx512-access.o gsnap_avx512-filestring.o gsnap_avx512-iit-read-univ.o gsnap_avx512-iit-read.o gsnap_avx512-bzip2.o gsnap_avx512-reader.o gsnap_avx512-genomicpos.o gsnap_avx512-compress.o gsnap_avx512-genome.o gsnap_avx512-transcriptome.o gsnap_avx512-popcount.o gsnap_avx512-genomebits.o gsnap_avx512-genomebits_consec.o gsnap_avx512-genomebits_count.o gsnap_avx512-genomebits_kmer.o gsnap_avx512-genomebits_indel.o gsnap_avx512-genomebits_decode.o gsnap_avx512-genomebits_mismatches.o gsnap_avx512-genomebits_trim.o gsnap_avx512-dinucl_bits.o gsnap_avx512-genome_sites.o gsnap_avx512-bitpack64-read.o gsnap_avx512-bitpack64-readtwo.o gsnap_avx512-mergeinfo.o gsnap_avx512-merge-diagonals-heap-uint4.o gsnap_avx512-merge-uint4.o gsnap_avx512-merge-diagonals-simd-uint4.o gsnap_avx512-indexdb.o gsnap_avx512-localdb-read.o gsnap_avx512-oligo.o gsnap_avx512-chrnum.o gsnap_avx512-maxent_hr.o gsnap_avx512-mapq.o gsnap_avx512-fopen.o gsnap_avx512-shortread.o gsnap_avx512-junction.o gsnap_avx512-concordance.o gsnap_avx512-simplepair.o gsnap_avx512-orderstat.o gsnap_avx512-intlistpool.o gsnap_avx512-uintlistpool.o gsnap_avx512-listpool.o gsnap_avx512-hitlistpool.o gsnap_avx512-pathpool.o gsnap_avx512-auxinfopool.o gsnap_avx512-pathstorepool.o gsnap_avx512-intron.o gsnap_avx512-gbuffer.o gsnap_avx512-select64-common.o gsnap_avx512-select64-ones.o gsnap_avx512-select64-zeroes.o gsnap_avx512-ef64.o gsnap_avx512-nr-x.o gsnap_avx512-knownsplicing.o gsnap_avx512-knownindels.o gsnap_avx512-splice.o gsnap_avx512-indel.o gsnap_avx512-spliceendsgen.o gsnap_avx512-spliceends.o gsnap_avx512-bitpack64-access.o gsnap_avx512-trdiag.o gsnap_avx512-trdiagpool.o gsnap_avx512-tr-extension-search.o gsnap_avx512-univdiag.o gsnap_avx512-univdiagpool.o gsnap_avx512-sedgesort.o gsnap_avx512-auxinfo.o gsnap_avx512-pathstore.o gsnap_avx512-altsplice.o gsnap_avx512-path.o gsnap_avx512-pathpair.o gsnap_avx512-path-solve.o gsnap_avx512-path-fusion.o gsnap_avx512-path-trim.o gsnap_avx512-path-eval.o gsnap_avx512-pathpair-eval.o gsnap_avx512-path-print-alignment.o gsnap_avx512-path-print-m8.o gsnap_avx512-path-print-sam.o gsnap_avx512-path-learn.o gsnap_avx512-method.o gsnap_avx512-doublelist.o gsnap_avx512-bitvector.o gsnap_avx512-transcriptpool.o gsnap_avx512-exon.o gsnap_avx512-transcript.o gsnap_avx512-trpathpool.o gsnap_avx512-trpath.o gsnap_avx512-trpath-solve.o gsnap_avx512-trpath-convert.o gsnap_avx512-trpath-eval.o gsnap_avx512-transcriptome-search.o gsnap_avx512-vectorpool.o gsnap_avx512-repair.o gsnap_avx512-transcript-remap.o gsnap_avx512-transcript-velocity.o gsnap_avx512-intersect-small.o gsnap_avx512-intersect-uint2.o gsnap_avx512-intersect-approx-uint4.o gsnap_avx512-intersect-approx-indices-uint4.o gsnap_avx512-intersect-wdups-indices.o gsnap_avx512-intersect-lower-small.o gsnap_avx512-intersect-higher-small.o gsnap_avx512-intersect-indices-small.o gsnap_avx512-intersect-indices2-small.o gsnap_avx512-intersect-concordance-uint4.o gsnap_avx512-kmer-search.o gsnap_avx512-extension-search.o gsnap_avx512-repetitive.o gsnap_avx512-uint8table.o gsnap_avx512-uinttable.o gsnap_avx512-stage1hr.o gsnap_avx512-stage1hr-single.o gsnap_avx512-stage1hr-paired.o gsnap_avx512-uinttableuint.o gsnap_avx512-tableuint.o gsnap_avx512-single-cell.o gsnap_avx512-request.o gsnap_avx512-resulthr.o gsnap_avx512-output.o gsnap_avx512-inbuffer.o gsnap_avx512-samheader.o gsnap_avx512-printbuffer.o gsnap_avx512-outbuffer.o gsnap_avx512-uintpairtable.o gsnap_avx512-splice-count.o gsnap_avx512-support.o gsnap_avx512-datadir.o gsnap_avx512-parserange.o gsnap_avx512-getline.o gsnap_avx512-gsnap.o -lz -lbz2 -lm gcc -DTARGET=\"x86_64-pc-linux-gnu\" -DGMAPDB=\"/var/cache/gmap\" -DGSNAP=1 -DLARGE_GENOMES=1 -mpopcnt -DHAVE_SSE2=1 -DHAVE_SSSE3=1 -DHAVE_SSE4_1=1 -DHAVE_SSE4_2=1 -DHAVE_AVX2=1 -DHAVE_AVX512=1 -msse2 -mssse3 -msse4.1 -msse4.2 -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/gmap-Yvd6ZU/gmap-2024-11-20+ds=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -O3 -DSIMDE_ENABLE_OPENMP -fomit-frame-pointer -Werror=implicit-function-declaration -Wl,-z,relro -Wl,-z,now -o gsnapl.avx512 gsnapl_avx512-except.o gsnapl_avx512-assert.o gsnapl_avx512-mem.o gsnapl_avx512-intlist.o gsnapl_avx512-uintlist.o gsnapl_avx512-uint8list.o gsnapl_avx512-list.o gsnapl_avx512-littleendian.o gsnapl_avx512-bigendian.o gsnapl_avx512-univinterval.o gsnapl_avx512-interval.o gsnapl_avx512-stopwatch.o gsnapl_avx512-semaphore.o gsnapl_avx512-access.o gsnapl_avx512-filestring.o gsnapl_avx512-iit-read-univ.o gsnapl_avx512-iit-read.o gsnapl_avx512-bzip2.o gsnapl_avx512-reader.o gsnapl_avx512-genomicpos.o gsnapl_avx512-compress.o gsnapl_avx512-genome.o gsnapl_avx512-transcriptome.o gsnapl_avx512-popcount.o gsnapl_avx512-genomebits.o gsnapl_avx512-genomebits_consec.o gsnapl_avx512-genomebits_count.o gsnapl_avx512-genomebits_kmer.o gsnapl_avx512-genomebits_indel.o gsnapl_avx512-genomebits_decode.o gsnapl_avx512-genomebits_mismatches.o gsnapl_avx512-genomebits_trim.o gsnapl_avx512-dinucl_bits.o gsnapl_avx512-genome_sites.o gsnapl_avx512-bitpack64-read.o gsnapl_avx512-bitpack64-readtwo.o gsnapl_avx512-mergeinfo.o gsnapl_avx512-merge-diagonals-heap-uint8.o gsnapl_avx512-merge-uint8.o gsnapl_avx512-merge-diagonals-simd-uint8.o gsnapl_avx512-merge-diagonals-heap-uint4.o gsnapl_avx512-merge-uint4.o gsnapl_avx512-merge-diagonals-simd-uint4.o gsnapl_avx512-indexdb.o gsnapl_avx512-localdb-read.o gsnapl_avx512-oligo.o gsnapl_avx512-chrnum.o gsnapl_avx512-maxent_hr.o gsnapl_avx512-mapq.o gsnapl_avx512-fopen.o gsnapl_avx512-shortread.o gsnapl_avx512-junction.o gsnapl_avx512-concordance.o gsnapl_avx512-simplepair.o gsnapl_avx512-orderstat.o gsnapl_avx512-intlistpool.o gsnapl_avx512-uintlistpool.o gsnapl_avx512-uint8listpool.o gsnapl_avx512-listpool.o gsnapl_avx512-hitlistpool.o gsnapl_avx512-pathpool.o gsnapl_avx512-auxinfopool.o gsnapl_avx512-pathstorepool.o gsnapl_avx512-intron.o gsnapl_avx512-gbuffer.o gsnapl_avx512-select64-common.o gsnapl_avx512-select64-ones.o gsnapl_avx512-select64-zeroes.o gsnapl_avx512-ef64.o gsnapl_avx512-nr-x.o gsnapl_avx512-knownsplicing.o gsnapl_avx512-knownindels.o gsnapl_avx512-splice.o gsnapl_avx512-indel.o gsnapl_avx512-spliceendsgen.o gsnapl_avx512-spliceends.o gsnapl_avx512-bitpack64-access.o gsnapl_avx512-trdiag.o gsnapl_avx512-trdiagpool.o gsnapl_avx512-tr-extension-search.o gsnapl_avx512-univdiag.o gsnapl_avx512-univdiagpool.o gsnapl_avx512-sedgesort.o gsnapl_avx512-auxinfo.o gsnapl_avx512-pathstore.o gsnapl_avx512-altsplice.o gsnapl_avx512-path.o gsnapl_avx512-pathpair.o gsnapl_avx512-path-solve.o gsnapl_avx512-path-fusion.o gsnapl_avx512-path-trim.o gsnapl_avx512-path-eval.o gsnapl_avx512-pathpair-eval.o gsnapl_avx512-path-print-alignment.o gsnapl_avx512-path-print-m8.o gsnapl_avx512-path-print-sam.o gsnapl_avx512-path-learn.o gsnapl_avx512-method.o gsnapl_avx512-doublelist.o gsnapl_avx512-bitvector.o gsnapl_avx512-transcriptpool.o gsnapl_avx512-exon.o gsnapl_avx512-transcript.o gsnapl_avx512-trpathpool.o gsnapl_avx512-trpath.o gsnapl_avx512-trpath-solve.o gsnapl_avx512-trpath-convert.o gsnapl_avx512-trpath-eval.o gsnapl_avx512-transcriptome-search.o gsnapl_avx512-vectorpool.o gsnapl_avx512-repair.o gsnapl_avx512-transcript-remap.o gsnapl_avx512-transcript-velocity.o gsnapl_avx512-intersect-large.o gsnapl_avx512-intersect-small.o gsnapl_avx512-intersect-uint2.o gsnapl_avx512-intersect-approx-uint4.o gsnapl_avx512-intersect-approx-uint8.o gsnapl_avx512-intersect-approx-indices-uint8.o gsnapl_avx512-intersect-wdups-indices.o gsnapl_avx512-intersect-lower-large.o gsnapl_avx512-intersect-higher-large.o gsnapl_avx512-intersect-indices-small.o gsnapl_avx512-intersect-indices2-large.o gsnapl_avx512-intersect-indices-uint8.o gsnapl_avx512-intersect-concordance-uint8.o gsnapl_avx512-kmer-search.o gsnapl_avx512-extension-search.o gsnapl_avx512-repetitive.o gsnapl_avx512-uint8table.o gsnapl_avx512-stage1hr.o gsnapl_avx512-stage1hr-single.o gsnapl_avx512-stage1hr-paired.o gsnapl_avx512-uint8tableuint.o gsnapl_avx512-tableuint.o gsnapl_avx512-single-cell.o gsnapl_avx512-request.o gsnapl_avx512-resulthr.o gsnapl_avx512-output.o gsnapl_avx512-inbuffer.o gsnapl_avx512-samheader.o gsnapl_avx512-printbuffer.o gsnapl_avx512-outbuffer.o gsnapl_avx512-uint8pairtable.o gsnapl_avx512-splice-count.o gsnapl_avx512-support.o gsnapl_avx512-datadir.o gsnapl_avx512-parserange.o gsnapl_avx512-getline.o gsnapl_avx512-gsnap.o -lz -lbz2 -lm make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' Making all in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' cp gmap_process.pl gmap_process cp gmap_build.pl gmap_build chmod +x gmap_process chmod +x gmap_build cp gmap_cat.pl gmap_cat cp md_coords.pl md_coords chmod +x gmap_cat chmod +x md_coords cp fa_coords.pl fa_coords cp psl_splicesites.pl psl_splicesites chmod +x psl_splicesites chmod +x fa_coords cp psl_introns.pl psl_introns cp psl_genes.pl psl_genes chmod +x psl_introns chmod +x psl_genes cp ensembl_genes.pl ensembl_genes cp gtf_splicesites.pl gtf_splicesites chmod +x ensembl_genes cp gtf_introns.pl gtf_introns chmod +x gtf_splicesites chmod +x gtf_introns cp gtf_genes.pl gtf_genes cp gtf_transcript_splicesites.pl gtf_transcript_splicesites chmod +x gtf_genes cp gff3_splicesites.pl gff3_splicesites chmod +x gtf_transcript_splicesites chmod +x gff3_splicesites cp gff3_introns.pl gff3_introns cp gff3_genes.pl gff3_genes chmod +x gff3_introns cp dbsnp_iit.pl dbsnp_iit chmod +x dbsnp_iit chmod +x gff3_genes cp gvf_iit.pl gvf_iit cp vcf_iit.pl vcf_iit chmod +x gvf_iit chmod +x vcf_iit make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' Making all in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' debian/rules override_dh_auto_test make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_auto_test --no-parallel cd build && make -j1 check "TESTSUITEFLAGS=-j1 --verbose" VERBOSE=1 make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' Making check in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' Making check in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' make[3]: Nothing to be done for 'check'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' Making check in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make check-TESTS make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[5]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' PASS: align.test PASS: coords1.test PASS: setup1.test PASS: iit.test ============================================================================ Testsuite summary for gmap 2024-11-20 ============================================================================ # TOTAL: 4 # PASS: 4 # SKIP: 0 # XFAIL: 0 # FAIL: 0 # XPASS: 0 # ERROR: 0 ============================================================================ make[5]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[3]: Nothing to be done for 'check-am'. make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' create-stamp debian/debhelper-build-stamp dh_testroot -O--builddir=build dh_prep -O--builddir=build debian/rules override_dh_auto_install make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' mkdir -p /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Mapping and Alignment Program' \ /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src/gmap |debian/filter.pl >/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Genomic Short-read Nucleotide Alignment Program' \ /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src/gsnap |debian/filter.pl >/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnap.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Mapping and Alignment Program' \ /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src/gmapl |debian/filter.pl >/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Large Genome Short-read Nucleotide Alignment Program' \ /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src/gsnapl |debian/filter.pl >/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gsnapl.1 /usr/bin/help2man --no-info --version-string=2024-11-20+ds-2 --name='Tool for genome database creation for GMAP or GSNAP' \ /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util/gmap_build |debian/filter.pl >/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/man/man1/gmap_build.1 dh_auto_install --builddir build_avx512 cd build_avx512 && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx512 gmapl.avx512 gsnap.avx512 gsnapl.avx512 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx512' dh_auto_install --builddir build_avx2 cd build_avx2 && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.avx2 gmapl.avx2 gsnap.avx2 gsnapl.avx2 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_avx2' dh_auto_install --builddir build_sse42 cd build_sse42 && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse42 gmapl.sse42 gsnap.sse42 gsnapl.sse42 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse42' dh_auto_install --builddir build_sse41 cd build_sse41 && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse41 gmapl.sse41 gsnap.sse41 gsnapl.sse41 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_sse41' dh_auto_install --builddir build_ssse3 cd build_ssse3 && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.ssse3 gmapl.ssse3 gsnap.ssse3 gsnapl.ssse3 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build_ssse3' dh_auto_install cd build && make -j2 install DESTDIR=/build/gmap-Yvd6ZU/gmap-2024-11-20\+ds/debian/gmap AM_UPDATE_INFO_DIR=no make[2]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' Making install in src make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c cpuid gmap gmapl get-genome gmapindex indexdb_cat iit_store iit_get iit_dump gsnap gsnapl snpindex cmetindex atoiindex trindex gmap.nosimd gmapl.nosimd gsnap.nosimd gsnapl.nosimd gmap.sse2 gmapl.sse2 gsnap.sse2 gsnapl.sse2 '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/src' Making install in util make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' make[4]: Nothing to be done for 'install-data-am'. /usr/bin/mkdir -p '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' /usr/bin/install -c gmap_process gmap_build gmap_cat md_coords fa_coords psl_splicesites psl_introns psl_genes ensembl_genes gtf_splicesites gtf_introns gtf_genes gtf_transcript_splicesites gff3_splicesites gff3_introns gff3_genes dbsnp_iit gvf_iit vcf_iit '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap' make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/util' Making install in tests make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[4]: Nothing to be done for 'install-exec-am'. make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build/tests' make[3]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[4]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[4]: Nothing to be done for 'install-exec-am'. /bin/bash /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/config/install-sh -d /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/var/cache/gmap make[4]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[3]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[2]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds/build' make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' debian/rules override_dh_install make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' mkdir -p debian/gmap/usr/bin dh_install for bin in `echo gmap gsnap gmap_build gmapl gsnapl; \ cd /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/lib/gmap/; \ ls -1 gmap*.* gsnap*.* `; do \ ln -s /usr/lib/gmap/$bin debian/gmap/usr/bin/$bin; \ done make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_installdocs -O--builddir=build dh_installchangelogs -O--builddir=build debian/rules override_dh_installexamples make[1]: Entering directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' mkdir /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples find tests/ -type f -print0 | xargs -0r sed -i \ -e 's@/build/gmap-Yvd6ZU/gmap-2024-11-20+ds@«buildpath»@g' \ -e 's@\#! /bin/bash@\#! /bin/sh@g' tar --sort=name \ --mtime="@1740521462" \ --owner=root --group=root --numeric-owner \ --mode=go=rX,u+rw,a-s \ --exclude='*/align.log' \ --exclude='*/Makefile' \ --exclude='*/Makefile.in' \ -cJf /build/gmap-Yvd6ZU/gmap-2024-11-20+ds/debian/gmap/usr/share/doc/gmap/examples/tests.tar.xz tests make[1]: Leaving directory '/build/gmap-Yvd6ZU/gmap-2024-11-20+ds' dh_installman -O--builddir=build dh_installsystemduser -O--builddir=build dh_lintian -O--builddir=build dh_perl -O--builddir=build dh_link -O--builddir=build dh_strip_nondeterminism -O--builddir=build dh_compress -O--builddir=build dh_fixperms -O--builddir=build dh_missing -O--builddir=build dh_dwz -a -O--builddir=build dh_strip -a -O--builddir=build dh_makeshlibs -a -O--builddir=build dh_shlibdeps -a -O--builddir=build dh_installdeb -O--builddir=build dh_gencontrol -O--builddir=build dh_md5sums -O--builddir=build dh_builddeb -O--builddir=build dpkg-deb: building package 'gmap' in '../gmap_2024-11-20+ds-2_amd64.deb'. dpkg-deb: building package 'gmap-dbgsym' in '../gmap-dbgsym_2024-11-20+ds-2_amd64.deb'. dpkg-genbuildinfo -O../gmap_2024-11-20+ds-2_amd64.buildinfo dpkg-genchanges -O../gmap_2024-11-20+ds-2_amd64.changes dpkg-genchanges: info: not including original source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: binary and diff upload (original source NOT included) -------------------------------------------------------------------------------- Build finished at 2025-06-30T15:15:44Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Mon, 30 Jun 2025 15:15:45 +0000 | +------------------------------------------------------------------------------+ gmap_2024-11-20+ds-2_amd64.changes: ----------------------------------- Format: 1.8 Date: Tue, 25 Feb 2025 23:11:02 +0100 Source: gmap Binary: gmap gmap-dbgsym Architecture: source amd64 Version: 2024-11-20+ds-2 Distribution: perl-5.40-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: gmap - spliced and SNP-tolerant alignment for mRNA and short reads Closes: 1096727 Changes: gmap (2024-11-20+ds-2) unstable; urgency=medium . * c23.patch: new: fix build failure with gcc 15. (Closes: #1096727) * d/control: declare compliance to standards version 4.7.1. Checksums-Sha1: 5a5d67b4dfb1d64d58d952b5611f70be190ae137 1279 gmap_2024-11-20+ds-2.dsc 001732a99ca0cb3a84ed45d077ad50f64a671dce 14072 gmap_2024-11-20+ds-2.debian.tar.xz 7273270b825a0e75e54a3bc5a735f393972a03f6 55912500 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 56a6044335479696ffd00f7e082227a95da4fb1d 5504 gmap_2024-11-20+ds-2_amd64.buildinfo c0b41c6adafa70c0f0f0596e338982da9ed204da 34667932 gmap_2024-11-20+ds-2_amd64.deb Checksums-Sha256: eb8c363739b3abfe57d93ed0e9b6b52c2b15c27abfdda0be3b3215f15f53d7a1 1279 gmap_2024-11-20+ds-2.dsc d89244d1a477a2d3ad344206fd7300bfed0afbbfd1281e833cefe53269035a57 14072 gmap_2024-11-20+ds-2.debian.tar.xz a337ad2e44ed4af8f964fde2f8502b6e71dc140a7985f47cda18bec84f22419b 55912500 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 28ca9f557d8ab9fa7a3191f6e4d492ce8f00d1c09b81fa0a83a3679871f4dede 5504 gmap_2024-11-20+ds-2_amd64.buildinfo 419c97b535f60480bce2d5d4c25477034d8660d39ad57b25591d34a295cde0d5 34667932 gmap_2024-11-20+ds-2_amd64.deb Files: 9ffa7a20d46c289005631e27de8453d2 1279 science optional gmap_2024-11-20+ds-2.dsc a07153820128f0f55d9d053bfc3d6aa2 14072 science optional gmap_2024-11-20+ds-2.debian.tar.xz 780f0c9337799630b36378998e8921eb 55912500 debug optional gmap-dbgsym_2024-11-20+ds-2_amd64.deb 790bb4da6fb365965381c0a768c5582c 5504 science optional gmap_2024-11-20+ds-2_amd64.buildinfo 9edc2389c6ec34fca5b2dfbf7b614ac6 34667932 science optional gmap_2024-11-20+ds-2_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Mon, 30 Jun 2025 15:15:45 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: gmap Binary: gmap gmap-dbgsym Architecture: amd64 source Version: 2024-11-20+ds-2 Checksums-Md5: 9ffa7a20d46c289005631e27de8453d2 1279 gmap_2024-11-20+ds-2.dsc 780f0c9337799630b36378998e8921eb 55912500 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 9edc2389c6ec34fca5b2dfbf7b614ac6 34667932 gmap_2024-11-20+ds-2_amd64.deb Checksums-Sha1: 5a5d67b4dfb1d64d58d952b5611f70be190ae137 1279 gmap_2024-11-20+ds-2.dsc 7273270b825a0e75e54a3bc5a735f393972a03f6 55912500 gmap-dbgsym_2024-11-20+ds-2_amd64.deb c0b41c6adafa70c0f0f0596e338982da9ed204da 34667932 gmap_2024-11-20+ds-2_amd64.deb Checksums-Sha256: eb8c363739b3abfe57d93ed0e9b6b52c2b15c27abfdda0be3b3215f15f53d7a1 1279 gmap_2024-11-20+ds-2.dsc a337ad2e44ed4af8f964fde2f8502b6e71dc140a7985f47cda18bec84f22419b 55912500 gmap-dbgsym_2024-11-20+ds-2_amd64.deb 419c97b535f60480bce2d5d4c25477034d8660d39ad57b25591d34a295cde0d5 34667932 gmap_2024-11-20+ds-2_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Mon, 30 Jun 2025 15:15:43 +0000 Build-Path: /build/gmap-Yvd6ZU/gmap-2024-11-20+ds Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: architecture-properties (= 0.2.6), autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 13.8), base-passwd (= 3.6.7), bash (= 5.2.37-2+b3), binutils (= 2.44-3), binutils-common (= 2.44-3), binutils-x86-64-linux-gnu (= 2.44-3), bsdextrautils (= 2.41-5), bsdutils (= 1:2.41-5), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:14.2.0-1), cpp-13 (= 13.4.0-1), cpp-13-x86-64-linux-gnu (= 13.4.0-1), cpp-14 (= 14.2.0-19), cpp-14-x86-64-linux-gnu (= 14.2.0-19), cpp-x86-64-linux-gnu (= 4:14.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.24.2), debianutils (= 5.23.1), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.1-2), diffutils (= 1:3.10-4), dpkg (= 1.22.20), dpkg-dev (= 1.22.20), dwz (= 0.15-1+b1), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:14.2.0-1), g++-14 (= 14.2.0-19), g++-14-x86-64-linux-gnu (= 14.2.0-19), g++-x86-64-linux-gnu (= 4:14.2.0-1), gcc (= 4:14.2.0-1), gcc-13 (= 13.4.0-1), gcc-13-base (= 13.4.0-1), gcc-13-x86-64-linux-gnu (= 13.4.0-1), gcc-14 (= 14.2.0-19), gcc-14-base (= 14.2.0-19), gcc-14-x86-64-linux-gnu (= 14.2.0-19), gcc-x86-64-linux-gnu (= 4:14.2.0-1), gettext (= 0.23.1-2), gettext-base (= 0.23.1-2), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), help2man (= 1.49.3), hostname (= 3.25), init-system-helpers (= 1.68), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 14.2.0-19), libatomic1 (= 14.2.0-19), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.2-2), libaudit1 (= 1:4.0.2-2+b2), libbinutils (= 2.44-3), libblkid1 (= 2.41-5), libbz2-1.0 (= 1.0.8-6), libbz2-dev (= 1.0.8-6), libc-bin (= 2.41-9), libc-dev-bin (= 2.41-9), libc6 (= 2.41-9), libc6-dev (= 2.41-9), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-9), libcc1-0 (= 14.2.0-19), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.44-3), libctf0 (= 2.44-3), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.279), libdebhelper-perl (= 13.24.2), libdpkg-perl (= 1.22.20), libelf1t64 (= 0.192-4), libfile-stripnondeterminism-perl (= 1.14.1-2), libgcc-13-dev (= 13.4.0-1), libgcc-14-dev (= 14.2.0-19), libgcc-s1 (= 14.2.0-19), libgdbm-compat4t64 (= 1.24-2), libgdbm6t64 (= 1.24-2), libgmp10 (= 2:6.3.0+dfsg-3), libgomp1 (= 14.2.0-19), libgprofng0 (= 2.44-3), libhwasan0 (= 14.2.0-19), libisl23 (= 0.27-1), libitm1 (= 14.2.0-19), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41-5), liblocale-gettext-perl (= 1.07-7+b2), liblsan0 (= 14.2.0-19), liblzma5 (= 5.8.1-1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41-5), libmpc3 (= 1.3.1-1+b3), libmpfr6 (= 4.2.2-1), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.45-1), libperl5.40 (= 5.40.1-4), libpipeline1 (= 1.5.8-1), libquadmath0 (= 14.2.0-19), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe1 (= 2.44-3), libsimde-dev (= 0.8.2-3), libsmartcols1 (= 2.41-5), libsqlite3-0 (= 3.46.1-6), libssl3t64 (= 3.5.0-2), libstdc++-14-dev (= 14.2.0-19), libstdc++6 (= 14.2.0-19), libsystemd0 (= 257.7-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-4), libtsan2 (= 14.2.0-19), libubsan1 (= 14.2.0-19), libuchardet0 (= 0.0.8-1+b2), libudev1 (= 257.7-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41-5), libxml2 (= 2.12.7+dfsg+really2.9.14-1), libzstd1 (= 1.5.7+dfsg-1), linux-libc-dev (= 6.12.33-1), m4 (= 1.4.19-8), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.0-2), patch (= 2.8-2), perl (= 5.40.1-4), perl-base (= 5.40.1-4), perl-modules-5.40 (= 5.40.1-4), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.25), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41-5), xz-utils (= 5.8.1-1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1), zlib1g-dev (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1740521462" +------------------------------------------------------------------------------+ | Package contents Mon, 30 Jun 2025 15:15:45 +0000 | +------------------------------------------------------------------------------+ gmap-dbgsym_2024-11-20+ds-2_amd64.deb ------------------------------------- new Debian package, version 2.0. size 55912500 bytes: control archive=2528 bytes. 2099 bytes, 12 lines control 4639 bytes, 44 lines md5sums Package: gmap-dbgsym Source: gmap Version: 2024-11-20+ds-2 Auto-Built-Package: debug-symbols Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 223869 Depends: gmap (= 2024-11-20+ds-2) Section: debug Priority: optional Description: debug symbols for gmap Build-Ids: 0059c8d2fd1f442a51522e3bfc19f95afe7192e3 00f164729f3b36f30ae6304dcae685994b5a424f 02b7f30ca8122aefc25620c527ae9acfdca89e59 02b808521f82da73fec5edda16c79656a1fbdaa0 1379e4f2822dbcaa90fa3d66e921ac032596db87 15854f0860b50a3ddbfb27b3742531c2faa9b45c 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34667932 bytes: control archive=2660 bytes. 918 bytes, 20 lines control 4473 bytes, 75 lines md5sums Package: gmap Version: 2024-11-20+ds-2 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 268791 Depends: perl:any, libbz2-1.0, libc6 (>= 2.34), zlib1g (>= 1:1.2.6) Section: science Priority: optional Homepage: http://research-pub.gene.com/gmap Description: spliced and SNP-tolerant alignment for mRNA and short reads This package contains the programs GMAP and GSNAP as well as utilities to manage genome databases in GMAP/GSNAP format. GMAP (Genomic Mapping and Alignment Program) is a tool for aligning EST, mRNA and cDNA sequences. GSNAP (Genomic Short-read Nucleotide Alignment Program) is a tool for aligning single-end and paired-end transcriptome reads. Both tools can use a database of * known splice sites and identify novel splice sites. * known single-nucleotide polymorphisms (SNPs). GSNAP can align bisulfite-treated DNA. drwxr-xr-x root/root 0 2025-02-25 22:11 ./ drwxr-xr-x root/root 0 2025-02-25 22:11 ./usr/ drwxr-xr-x root/root 0 2025-02-25 22:11 ./usr/bin/ lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap -> ../lib/gmap/gmap lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.avx2 -> ../lib/gmap/gmap.avx2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.avx512 -> ../lib/gmap/gmap.avx512 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.nosimd -> ../lib/gmap/gmap.nosimd lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.sse2 -> ../lib/gmap/gmap.sse2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.sse41 -> ../lib/gmap/gmap.sse41 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.sse42 -> ../lib/gmap/gmap.sse42 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap.ssse3 -> ../lib/gmap/gmap.ssse3 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmap_build -> ../lib/gmap/gmap_build lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl -> ../lib/gmap/gmapl lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.avx2 -> ../lib/gmap/gmapl.avx2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.avx512 -> ../lib/gmap/gmapl.avx512 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.nosimd -> ../lib/gmap/gmapl.nosimd lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.sse2 -> ../lib/gmap/gmapl.sse2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.sse41 -> ../lib/gmap/gmapl.sse41 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.sse42 -> ../lib/gmap/gmapl.sse42 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gmapl.ssse3 -> ../lib/gmap/gmapl.ssse3 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap -> ../lib/gmap/gsnap lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.avx2 -> ../lib/gmap/gsnap.avx2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.avx512 -> ../lib/gmap/gsnap.avx512 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.nosimd -> ../lib/gmap/gsnap.nosimd lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.sse2 -> ../lib/gmap/gsnap.sse2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.sse41 -> ../lib/gmap/gsnap.sse41 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.sse42 -> ../lib/gmap/gsnap.sse42 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnap.ssse3 -> ../lib/gmap/gsnap.ssse3 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl -> ../lib/gmap/gsnapl lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.avx2 -> ../lib/gmap/gsnapl.avx2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.avx512 -> ../lib/gmap/gsnapl.avx512 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.nosimd -> ../lib/gmap/gsnapl.nosimd lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.sse2 -> ../lib/gmap/gsnapl.sse2 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.sse41 -> ../lib/gmap/gsnapl.sse41 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.sse42 -> ../lib/gmap/gsnapl.sse42 lrwxrwxrwx root/root 0 2025-02-25 22:11 ./usr/bin/gsnapl.ssse3 -> ../lib/gmap/gsnapl.ssse3 drwxr-xr-x root/root 0 2025-02-25 22:11 ./usr/lib/ drwxr-xr-x root/root 0 2025-02-25 22:11 ./usr/lib/gmap/ -rwxr-xr-x root/root 4242112 2025-02-25 22:11 ./usr/lib/gmap/atoiindex -rwxr-xr-x root/root 4242112 2025-02-25 22:11 ./usr/lib/gmap/cmetindex -rwxr-xr-x root/root 14568 2025-02-25 22:11 ./usr/lib/gmap/cpuid -rwxr-xr-x root/root 7863 2025-02-25 22:11 ./usr/lib/gmap/dbsnp_iit -rwxr-xr-x root/root 1256 2025-02-25 22:11 ./usr/lib/gmap/ensembl_genes -rwxr-xr-x root/root 21838 2025-02-25 22:11 ./usr/lib/gmap/fa_coords -rwxr-xr-x root/root 2977248 2025-02-25 22:11 ./usr/lib/gmap/get-genome -rwxr-xr-x root/root 16673 2025-02-25 22:11 ./usr/lib/gmap/gff3_genes -rwxr-xr-x root/root 14312 2025-02-25 22:11 ./usr/lib/gmap/gff3_introns -rwxr-xr-x root/root 15883 2025-02-25 22:11 ./usr/lib/gmap/gff3_splicesites -rwxr-xr-x root/root 14568 2025-02-25 22:11 ./usr/lib/gmap/gmap 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./usr/share/man/man1/gmapl.1.gz -rw-r--r-- root/root 6882 2025-02-25 22:11 ./usr/share/man/man1/gsnap.1.gz -rw-r--r-- root/root 6888 2025-02-25 22:11 ./usr/share/man/man1/gsnapl.1.gz drwxr-xr-x root/root 0 2025-02-25 22:11 ./var/ drwxr-xr-x root/root 0 2025-02-25 22:11 ./var/cache/ drwxr-xr-x root/root 0 2025-02-25 22:11 ./var/cache/gmap/ +------------------------------------------------------------------------------+ | Post Build Mon, 30 Jun 2025 15:15:47 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Mon, 30 Jun 2025 15:15:47 +0000 | +------------------------------------------------------------------------------+ Purging /build/gmap-Yvd6ZU Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Mon, 30 Jun 2025 15:15:48 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 2487172 Build-Time: 2702 Distribution: perl-5.40-throwaway Host Architecture: amd64 Install-Time: 5 Job: /srv/debomatic/incoming/gmap_2024-11-20+ds-2.dsc Machine Architecture: amd64 Package: gmap Package-Time: 2714 Source-Version: 2024-11-20+ds-2 Space: 2487172 Status: successful Version: 2024-11-20+ds-2 -------------------------------------------------------------------------------- Finished at 2025-06-30T15:15:44Z Build needed 00:45:14, 2487172k disk space