sbuild (Debian sbuild) 0.89.1 (28 April 2025) on carme.larted.org.uk +==============================================================================+ | mafft 7.525-1 (amd64) Fri, 05 Sep 2025 16:01:35 +0000 | +==============================================================================+ Package: mafft Version: 7.525-1 Source Version: 7.525-1 Distribution: perl-5.42-throwaway Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: full I: Setting up the chroot... I: Creating chroot session... I: Setting up log color... +------------------------------------------------------------------------------+ | Chroot Setup Commands Fri, 05 Sep 2025 16:01:35 +0000 | +------------------------------------------------------------------------------+ /usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mafft_7.525-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/chroot-setup-commands/dpkg-speedup mafft_7.525-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- I: Setting up apt archive... +------------------------------------------------------------------------------+ | Update chroot Fri, 05 Sep 2025 16:01:35 +0000 | +------------------------------------------------------------------------------+ Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:2 http://deb.debian.org/debian unstable InRelease Get:1 file:/srv/reprepro perl-5.42 InRelease [3042 B] Hit:3 http://deb.debian.org/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | Fetch source files Fri, 05 Sep 2025 16:01:37 +0000 | +------------------------------------------------------------------------------+ Local sources ------------- /srv/debomatic/incoming/mafft_7.525-1.dsc exists in /srv/debomatic/incoming; copying to chroot +------------------------------------------------------------------------------+ | Install package build dependencies Fri, 05 Sep 2025 16:01:38 +0000 | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), build-essential Filtered Build-Depends: debhelper-compat (= 13), build-essential dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ InRelease Get:2 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ Release [609 B] Ign:3 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ Release.gpg Get:4 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ Sources [600 B] Get:5 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ Packages [639 B] Fetched 1848 B in 0s (160 kB/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc dh-make gettext-doc libasprintf-dev libgettextpo-dev gnulib-l10n groff libtool-doc gfortran | fortran95-compiler m4-doc apparmor less www-browser libmail-box-perl Recommended packages: curl | wget | lynx libarchive-cpio-perl libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdextrautils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base intltool-debian libarchive-zip-perl libdebhelper-perl libelf1t64 libfile-stripnondeterminism-perl libmagic-mgc libmagic1t64 libpipeline1 libtool libuchardet0 libxml2-16 m4 man-db po-debconf sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 10.7 MB of archives. After this operation, 40.6 MB of additional disk space will be used. Get:1 copy:/build/mafft-QKGPm6/resolver-xcnGlb/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [856 B] Get:2 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get:3 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get:4 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get:5 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.46-5 [43.6 kB] Get:6 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get:7 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get:8 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get:9 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.41.1-2 [95.0 kB] Get:10 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:11 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get:12 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.20-1 [324 kB] Get:13 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3.1 [494 kB] Get:14 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get:15 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.17-4 [862 kB] Get:16 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.23.1-2 [770 kB] Get:17 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.26 [91.8 kB] Get:18 http://deb.debian.org/debian unstable/main amd64 libtool all 2.5.4-5 [540 kB] Get:19 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:20 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:21 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.2-1 [19.8 kB] Get:22 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.2-1 [8768 B] Get:23 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.193-2 [193 kB] Get:24 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.16-2 [108 kB] Get:25 http://deb.debian.org/debian unstable/main amd64 libxml2-16 amd64 2.14.5+dfsg-0.2 [638 kB] Get:26 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get:27 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:28 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:29 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.26 [939 kB] Preconfiguring packages ... Fetched 10.7 MB in 0s (141 MB/s) Selecting previously unselected package sensible-utils. (Reading database ... 16171 files and directories currently installed.) Preparing to unpack .../00-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../01-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../02-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../03-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../04-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. 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Setting up libarchive-zip-perl (1.68-1) ... Setting up libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Setting up libdebhelper-perl (13.26) ... Setting up libmagic1t64:amd64 (1:5.46-5) ... Setting up gettext-base (0.23.1-2+b1) ... Setting up m4 (1.4.20-1) ... Setting up file (1:5.46-5) ... Setting up libelf1t64:amd64 (0.193-2) ... Setting up autotools-dev (20240727.1) ... Setting up autopoint (0.23.1-2) ... Setting up autoconf (2.72-3.1) ... Setting up dwz (0.16-2) ... Setting up sensible-utils (0.0.26) ... Setting up libuchardet0:amd64 (0.0.8-2) ... Setting up automake (1:1.17-4) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.2-1) ... Setting up gettext (0.23.1-2+b1) ... Setting up libtool (2.5.4-5) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up dh-strip-nondeterminism (1.14.2-1) ... Setting up groff-base (1.23.0-9) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up debhelper (13.26) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.41-12) ... +------------------------------------------------------------------------------+ | Check architectures Fri, 05 Sep 2025 16:01:42 +0000 | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any) +------------------------------------------------------------------------------+ | Build environment Fri, 05 Sep 2025 16:01:42 +0000 | +------------------------------------------------------------------------------+ Kernel: Linux 6.12.25-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.25-1 (2025-04-25) amd64 (x86_64) Toolchain package versions: binutils_2.45-6 dpkg-dev_1.22.21 g++-14_14.3.0-6 g++-15_15.2.0-3 gcc-14_14.3.0-6 gcc-15_15.2.0-3 libc6-dev_2.41-12 libstdc++-14-dev_14.3.0-6 libstdc++-15-dev_15.2.0-3 libstdc++6_15.2.0-3 linux-libc-dev_6.16.3-1 Package versions: adduser_3.152 apt_3.1.5 autoconf_2.72-3.1 automake_1:1.17-4 autopoint_0.23.1-2 autotools-dev_20240727.1 base-files_14 base-passwd_3.6.7 bash_5.3-1 binutils_2.45-6 binutils-common_2.45-6 binutils-gold_2.44-2 binutils-gold-x86-64-linux-gnu_2.44-2 binutils-x86-64-linux-gnu_2.45-6 bsdextrautils_2.41.1-2 bsdutils_1:2.41.1-2 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.7-3 cpp_4:15.2.0-1 cpp-14_14.3.0-6 cpp-14-x86-64-linux-gnu_14.3.0-6 cpp-15_15.2.0-3 cpp-15-x86-64-linux-gnu_15.2.0-3 cpp-x86-64-linux-gnu_4:15.2.0-1 dash_0.5.12-12 debconf_1.5.91 debhelper_13.26 debian-archive-keyring_2025.1 debianutils_5.23.2 dh-autoreconf_20 dh-strip-nondeterminism_1.14.2-1 diffutils_1:3.10-4 dirmngr_2.4.8-3 dpkg_1.22.21 dpkg-dev_1.22.21 dwz_0.16-2 eatmydata_131-2 file_1:5.46-5 findutils_4.10.0-3 g++_4:15.2.0-1 g++-14_14.3.0-6 g++-14-x86-64-linux-gnu_14.3.0-6 g++-15_15.2.0-3 g++-15-x86-64-linux-gnu_15.2.0-3 g++-x86-64-linux-gnu_4:15.2.0-1 gcc_4:15.2.0-1 gcc-14_14.3.0-6 gcc-14-base_14.3.0-6 gcc-14-x86-64-linux-gnu_14.3.0-6 gcc-15_15.2.0-3 gcc-15-base_15.2.0-3 gcc-15-x86-64-linux-gnu_15.2.0-3 gcc-x86-64-linux-gnu_4:15.2.0-1 gettext_0.23.1-2+b1 gettext-base_0.23.1-2+b1 gnupg_2.4.8-3 gnupg-l10n_2.4.8-3 gpg_2.4.8-3 gpg-agent_2.4.8-3 gpgconf_2.4.8-3 gpgsm_2.4.8-3 grep_3.11-4 groff-base_1.23.0-9 gzip_1.13-1 hostname_3.25 init-system-helpers_1.69 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg7.0_3.1.5 libarchive-zip-perl_1.68-1 libasan8_15.2.0-3 libassuan9_3.0.2-2 libatomic1_15.2.0-3 libattr1_1:2.5.2-3 libaudit-common_1:4.0.5-1 libaudit1_1:4.0.5-1 libbinutils_2.45-6 libblkid1_2.41.1-2 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.41-12 libc-dev-bin_2.41-12 libc6_2.41-12 libc6-dev_2.41-12 libcap-ng0_0.8.5-4+b1 libcap2_1:2.75-10+b1 libcc1-0_15.2.0-3 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.45-6 libctf0_2.45-6 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.280 libdebhelper-perl_13.26 libdpkg-perl_1.22.21 libeatmydata1_131-2+b1 libelf1t64_0.193-2 libffi8_3.5.2-2 libfile-stripnondeterminism-perl_1.14.2-1 libgcc-14-dev_14.3.0-6 libgcc-15-dev_15.2.0-3 libgcc-s1_15.2.0-3 libgcrypt20_1.11.2-2 libgdbm-compat4t64_1.26-1 libgdbm6t64_1.26-1 libgmp10_2:6.3.0+dfsg-5 libgnutls30t64_3.8.10-2 libgomp1_15.2.0-3 libgpg-error0_1.55-2 libgprofng0_2.45-6 libhogweed6t64_3.10.1-1 libhwasan0_15.2.0-3 libidn2-0_2.3.8-4 libisl23_0.27-1 libitm1_15.2.0-3 libjansson4_2.14-2+b3 libksba8_1.6.7-2+b1 liblastlog2-2_2.41.1-2 libldap2_2.6.10+dfsg-1+b1 liblsan0_15.2.0-3 liblz4-1_1.10.0-4 liblzma5_5.8.1-1.1 libmagic-mgc_1:5.46-5 libmagic1t64_1:5.46-5 libmd0_1.1.0-2+b1 libmount1_2.41.1-2 libmpc3_1.3.1-2 libmpfr6_4.2.2-2 libncursesw6_6.5+20250216-2 libnettle8t64_3.10.1-1 libnpth0t64_1.8-3 libp11-kit0_0.25.5-3 libpam-modules_1.7.0-5 libpam-modules-bin_1.7.0-5 libpam-runtime_1.7.0-5 libpam0g_1.7.0-5 libpcre2-8-0_10.46-1 libperl5.40_5.40.1-6 libperl5.42_5.42.0-2 libpipeline1_1.5.8-1 libquadmath0_15.2.0-3 libreadline8t64_8.3-2 libsasl2-2_2.1.28+dfsg1-9 libsasl2-modules-db_2.1.28+dfsg1-9 libseccomp2_2.6.0-2 libselinux1_3.8.1-1 libsemanage-common_3.8.1-1 libsemanage2_3.8.1-1 libsepol2_3.8.1-1 libsframe2_2.45-6 libsmartcols1_2.41.1-2 libsqlite3-0_3.46.1-7 libssl3t64_3.5.2-1 libstdc++-14-dev_14.3.0-6 libstdc++-15-dev_15.2.0-3 libstdc++6_15.2.0-3 libsystemd0_258~rc4-1 libtasn1-6_4.20.0-2 libtinfo6_6.5+20250216-2 libtool_2.5.4-5 libtsan2_15.2.0-3 libubsan1_15.2.0-3 libuchardet0_0.0.8-2 libudev1_258~rc4-1 libunistring5_1.3-2 libuuid1_2.41.1-2 libxml2-16_2.14.5+dfsg-0.2 libxxhash0_0.8.3-2 libzstd1_1.5.7+dfsg-1.1 linux-libc-dev_6.16.3-1 login.defs_1:4.18.0-1 m4_1.4.20-1 make_4.4.1-2 man-db_2.13.1-1 mawk_1.3.4.20250131-1 ncurses-base_6.5+20250216-2 ncurses-bin_6.5+20250216-2 openssl-provider-legacy_3.5.2-1 passwd_1:4.18.0-1 patch_2.8-2 perl_5.42.0-2 perl-base_5.42.0-2 perl-modules-5.40_5.40.1-6 perl-modules-5.42_5.42.0-2 pinentry-curses_1.3.2-3 po-debconf_1.0.21+nmu1 readline-common_8.3-2 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.26 sqv_1.3.0-3 sysvinit-utils_3.14-4 tar_1.35+dfsg-3.1 util-linux_2.41.1-2 xz-utils_5.8.1-1.1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build Fri, 05 Sep 2025 16:01:42 +0000 | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: mafft Binary: mafft Architecture: any Version: 7.525-1 Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Andreas Tille Homepage: https://mafft.cbrc.jp/alignment/software/ Standards-Version: 4.7.2 Vcs-Browser: https://salsa.debian.org/med-team/mafft Vcs-Git: https://salsa.debian.org/med-team/mafft.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13) Package-List: mafft deb science optional arch=any Checksums-Sha1: a87733c60bb169d1945d0b040891acbc6562724a 622798 mafft_7.525.orig.tar.gz fb7627482b78b4831ed1e2a49300f1e8af519ae8 8188 mafft_7.525-1.debian.tar.xz Checksums-Sha256: edb34ae9b26d6b55328c18fa060ed741bca8cd599c2f4f8fad0e0871c8082265 622798 mafft_7.525.orig.tar.gz c85f33560c59178f14844814f0d009cc7bbd485dc4db0d38c185fbe5dcb67073 8188 mafft_7.525-1.debian.tar.xz Files: 0692b3874b73f8b93be204fcfc542254 622798 mafft_7.525.orig.tar.gz 29fe54251799ef332224aebb8ffc4de7 8188 mafft_7.525-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJGBAEBCgAwFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmi6uMwSHGNydXNvZUBk ZWJpYW4ub3JnAAoJEDwmdj9sZ+bivjYP/RIfha+I7VyzLde0Osp21GU3p+2yJk58 iwirUu7cKZFe/h9VPnXlToNIJ+7sfbbms8r+/6y/OFYTLUj7vgJOZT+JGbGbE+9c XNkiT7m87uRk5JYSicr3QWY853msmWet+/slcYmDpL56AeuG/ssM6IkoHGqQqFfd Gq/d/rflDLfMxfEMnRmpFtokNcfGWZTIjk52l+z2uV9Kfn6SNsWgormDN1Ph79HF tQFFBjmyNf27aVJ5TUCGTaJLkUfpeGwtGsU2shIIIx/Bwo2rVDNfj0ZbGL9q/m2A A7fnnpGR1JqBU34S9co8SZzlXTEoRPAeO2uNST+97wsnFmsA+dPlHVw6n2wKH1mH V3KTo1IIAjzp0KOr8HS4yv0aZTUDZHGJSO4JxvgmH2FNxFZsxBp83RlUX5IkwKPF hBp8r+Zdp0DDj0ALFy37a9EqS0OK3Vt4lnGKoa8vjXsKwoCLkX1MRDa1xFt1laSH 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mafft_7.525-1 perl-5.42-throwaway amd64 -------------------------------------------------------------------------------------------------------------- I: Finished running '/usr/share/debomatic/sbuildcommands/starting-build-commands/no-network mafft_7.525-1 perl-5.42-throwaway amd64'. Finished processing commands. -------------------------------------------------------------------------------- User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LC_ALL=C.UTF-8 LD_LIBRARY_PATH=/usr/lib/libeatmydata LD_PRELOAD=libeatmydata.so LOGNAME=debomatic PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games PWD=/build/mafft-QKGPm6/mafft-7.525 SCHROOT_ALIAS_NAME=perl-5.42-throwaway-amd64-debomatic SCHROOT_CHROOT_NAME=perl-5.42-amd64-debomatic SCHROOT_COMMAND=env SCHROOT_GID=110 SCHROOT_GROUP=sbuild SCHROOT_SESSION_ID=perl-5.42-amd64-debomatic-13d8b41c-5d3c-4ead-9fc2-cb7a444350af SCHROOT_UID=1002 SCHROOT_USER=debomatic SHELL=/bin/sh USER=debomatic dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -us -uc -Zxz dpkg-buildpackage: info: source package mafft dpkg-buildpackage: info: source version 7.525-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source -Zxz --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean --sourcedirectory=core dh_auto_clean -O--sourcedirectory=core cd core && make -j2 clean make[1]: Entering directory '/build/mafft-QKGPm6/mafft-7.525/core' rm -f *.o *.a *.exe *~ mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version mafft mafft-homologs.rb mafft-sparsecore.rb libdisttbfast.so libdisttbfast.dylib libdisttbfast.dll *.gcda *.gcno make[1]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525/core' dh_autoreconf_clean -O--sourcedirectory=core debian/rules override_dh_clean make[1]: Entering directory '/build/mafft-QKGPm6/mafft-7.525' rm -rf binaries/* scripts/* dh_clean make[1]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525' dpkg-source -Zxz -b . dpkg-source: info: using source format '3.0 (quilt)' dpkg-source: info: building mafft using existing ./mafft_7.525.orig.tar.gz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: building mafft in mafft_7.525-1.debian.tar.xz dpkg-source: info: building mafft in mafft_7.525-1.dsc debian/rules binary dh binary --sourcedirectory=core dh_update_autotools_config -O--sourcedirectory=core dh_autoreconf -O--sourcedirectory=core dh_auto_configure -O--sourcedirectory=core debian/rules override_dh_auto_build make[1]: Entering directory '/build/mafft-QKGPm6/mafft-7.525' dh_auto_build -- \ PREFIX=/usr/lib/mafft \ ENABLE_MULTITHREAD=-Denablemultithread \ LIBDIR=/usr/lib/mafft/lib/mafft \ CFLAGS="-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" \ LDFLAGS="-Wl,-z,relro -Wl,-z,now" cd core && make -j2 "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft ENABLE_MULTITHREAD=-Denablemultithread LIBDIR=/usr/lib/mafft/lib/mafft "CFLAGS=-g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2" "LDFLAGS=-Wl,-z,relro -Wl,-z,now" make[2]: Entering directory '/build/mafft-QKGPm6/mafft-7.525/core' cp mafftash_premafft.tmpl mafftash_premafft.pl cp seekquencer_premafft.tmpl seekquencer_premafft.pl gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mtxutl.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c io.c io.c: In function ‘PreRead’: io.c:1120:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1120 | fgets( b, B-1, fp ); *locnjob = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c:1125:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1125 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1129:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1129 | fgets( b, B-1, fp ); nleni = atoi( b ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘FRead’: io.c:1165:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1165 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:1255:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1255 | fgets( b, B-1, fp ); nlen[i] = atoi( b ); /* seq i no nagasa */ | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf_part_pointer’: io.c:2708:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2708 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2710:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2710 | fgets( b, B, fp ); nseq0 = atoi( b ); // 2020/Oct/23 | ^~~~~~~~~~~~~~~~~ io.c:2716:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2716 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf_pointer’: io.c:2746:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2746 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2747:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2747 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) | ^~~~~~~~~~~~~~~~~ io.c:2752:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2752 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_doublehalf’: io.c:2780:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2780 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2781:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2781 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2782:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2782 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_double’: io.c:2810:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2810 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2811:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2811 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2812:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2812 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_int’: io.c:2840:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2840 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2841:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2841 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2842:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2842 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2_pointer’: io.c:2871:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2871 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2872:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2872 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2873:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2873 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘readhat2’: io.c:2901:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2901 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c:2902:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2902 | fgets( b, B, fp ); b[5] = 0; nseq0 = atoi( b ); if( nseq != nseq0 ) ErrorExit( "hat2 is wrong." ); | ^~~~~~~~~~~~~~~~~ io.c:2903:5: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2903 | fgets( b, B, fp ); | ^~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta_sub’: io.c:3158:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3158 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3173:13: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3173 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadSsearch’: io.c:3192:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3192 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7_avscore’: io.c:3320:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3320 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3327:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3327 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3328:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3328 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7_scoreonly’: io.c:3443:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3443 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3450:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3450 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3451:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3451 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadBlastm7’: io.c:3561:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3561 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3568:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3568 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3569:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3569 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34noalign’: io.c:3593:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3593 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_nuc’: io.c:3630:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3630 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3656:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3656 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10’: io.c:3769:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3769 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:3793:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3793 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly_nucbk’: io.c:3896:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3896 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly_nuc’: io.c:3946:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3946 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34m10_scoreonly’: io.c:4007:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4007 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta34’: io.c:4063:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4063 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c:4089:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4089 | fgets( b, B-1, fp ); // initn: | ^~~~~~~~~~~~~~~~~~~ io.c:4092:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4092 | fgets( b, B-1, fp ); // Smith-Waterman score | ^~~~~~~~~~~~~~~~~~~ io.c:4104:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4104 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta3’: io.c:4126:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4126 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadFasta’: io.c:4151:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4151 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadOpt’: io.c:4188:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4188 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘ReadOpt2’: io.c:4209:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4209 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘readOtherOptions’: io.c:4305:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4305 | fgets( b, B-1, fp ); | ^~~~~~~~~~~~~~~~~~~ io.c: In function ‘loadaamtx’: io.c:5564:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5564 | fgets( inorder, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5596:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5596 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5619:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5619 | fgets( line, 999, mf ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readsubalignmentstable’: io.c:5775:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5775 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c:5796:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5796 | fgets( line, linelen-1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readmccaskill’: io.c:5850:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5850 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5860:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5860 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readpairfoldalign’: io.c:5919:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5919 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5932:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5932 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5939:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5939 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5953:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5953 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c:5959:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 5959 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ io.c: In function ‘readexternalanchors’: io.c:6397:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 6397 | fgets( buf, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mltaln9.c mltaln9.c: In function ‘check_guidetreefile’: mltaln9.c:2850:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 2850 | fgets( string, sizeof(string) / sizeof(char), fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘readlocalhomtable2_single_bin_noseek’: mltaln9.c:15688:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 15688 | fread( &size, sizeof( int ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15689:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 15689 | fread( &opt, sizeof( double ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15692:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 15692 | fread( m, size*sizeof( int ), 3, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c:15728:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 15728 | fread( &c, sizeof( char ), 1, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mltaln9.c: In function ‘fixed_musclesupg_double_realloc_nobk_halfmtx_treeout_memsave’: mltaln9.c:6494:28: warning: argument 2 range [18446744071562067968, 18446744073709551615] exceeds maximum object size 9223372036854775807 [-Walloc-size-larger-than=] 6494 | int *mem = calloc( sizeof( int ), nseq ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from mltaln.h:13, from mltaln9.c:1: /usr/include/stdlib.h:675:14: note: in a call to allocation function ‘calloc’ declared here 675 | extern void *calloc (size_t __nmemb, size_t __size) | ^~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c tddis.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c constants.c In file included from constants.c:7: blosum.c: In function ‘overridematrix’: blosum.c:372:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 372 | fgets( buf, 499, fp ); | ^~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c nj.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c partSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c rna.c rna.c: In function ‘rnaalifoldcall’: rna.c:225:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 225 | system( cmd ); | ^~~~~~~~~~~~~ rna.c:245:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 245 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ rna.c:285:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 285 | system( cmd ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Salignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Dalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Falign_localhom.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Galign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c Lalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c genalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalignmm.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c fftFunctions.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c fft.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c tditeration.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dvtditr.c dvtditr.c: In function ‘main’: dvtditr.c:1020:33: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1020 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c defs.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c SAalignmm.c -o SAalignmm.o gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c treeOperation.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c addfunctions.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dndfast7.c dndfast7.c: In function ‘main’: dndfast7.c:326:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 326 | system( com ); | ^~~~~~~~~~~~~ gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o dndblast.o dndblast.c dndblast.c: In function ‘main’: dndblast.c:201:25: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 201 | system( com ); | ^~~~~~~~~~~~~ dndblast.c:382:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 382 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c sextet5.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-distance.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c MSalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c suboptalign11.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalignmain.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c pairlocalalign.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c multi2hat3s.c pairlocalalign.c: In function ‘calllast_once’: pairlocalalign.c:1056:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1056 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c:1092:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1092 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readlastresx’: pairlocalalign.c:608:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 608 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘calllast_fast’: pairlocalalign.c:981:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 981 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘lastcallthread’: pairlocalalign.c:872:33: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 872 | system( command ); | ^~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readlastresx_singleq’: pairlocalalign.c:374:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 374 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘readhat4’: pairlocalalign.c:1532:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1532 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1544:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1544 | fgets( oneline, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘recalllara’: pairlocalalign.c:1245:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1245 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘callmxscarna_giving_bpp’: pairlocalalign.c:1408:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1408 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1410:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1410 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1430:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1430 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1451:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1451 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1465:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1465 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1485:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1485 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1487:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1487 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘calldafs_giving_bpp’: pairlocalalign.c:1291:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1291 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1293:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1293 | system( com ); | ^~~~~~~~~~~~~ pairlocalalign.c:1313:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1313 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1334:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1334 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1344:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1344 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ pairlocalalign.c:1364:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1364 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1366:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1366 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:1368:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 1368 | fgets( com, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c: In function ‘pairalign_node’: pairlocalalign.c:3468:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3468 | system( "rm -rf hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3469:9: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3469 | system( "mkdir hat3dir" ); // toriaezu | ^~~~~~~~~~~~~~~~~~~~~~~~~ pairlocalalign.c:3474:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3474 | system( fn ); | ^~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c pairash.c pairash.c: In function ‘prepareash’: pairash.c:639:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 639 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:681:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 681 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash’: pairash.c:485:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 485 | system( com ); | ^~~~~~~~~~~~~ pairash.c: In function ‘readrash’: pairash.c:277:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 277 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:284:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 284 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:289:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 289 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:294:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 294 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘preparetmalign’: pairash.c:530:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 530 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:576:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 576 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:587:25: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 587 | system( command ); | ^~~~~~~~~~~~~~~~~ pairash.c: In function ‘checkcbeta’: pairash.c:321:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 321 | fgets( linec, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign’: pairash.c:347:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 347 | system( com ); | ^~~~~~~~~~~~~ pairash.c:356:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 356 | fgets( com, 100, fp ); | ^~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘readtmalign’: pairash.c:228:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 228 | fgets( line, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ pairash.c:232:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 232 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:235:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 235 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c:238:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 238 | fgets( line, nlenmax*2, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash.isra’: pairash.c:428:43: warning: ‘.’ directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 428 | sprintf( cachefile, "%s/%s.%s.rash", cachedir, fname1, fname2 ); | ^ In file included from /usr/include/stdio.h:970, from mltaln.h:12, from pairash.c:1: In function ‘sprintf’, inlined from ‘callrash.isra’ at pairash.c:428:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 8 or more bytes (assuming 10007) into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pairash.c: In function ‘callrash.isra’: pairash.c:484:36: warning: ‘%s’ directive writing up to 9999 bytes into a region of size 9996 [-Wformat-overflow=] 484 | sprintf( com, "cat %s > %s.rashout", cachefile, pairid ); | ^~ ~~~~~~~~~ In function ‘sprintf’, inlined from ‘callrash.isra’ at pairash.c:484:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 16 and 11014 bytes into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign.isra’: pairash.c:346:41: warning: ‘%s’ directive writing up to 9999 bytes into a region of size 9991 [-Wformat-overflow=] 346 | sprintf( com, "mkdir -p %s", cachedir ); | ^~ ~~~~~~~~ In function ‘sprintf’, inlined from ‘calltmalign.isra’ at pairash.c:346:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output between 10 and 10009 bytes into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ pairash.c: In function ‘calltmalign.isra’: pairash.c:349:45: warning: ‘-’ directive writing 1 byte into a region of size between 0 and 9999 [-Wformat-overflow=] 349 | sprintf( cachefile, "%s/%s%s-%s%s", cachedir, fname1, chain1, fname2, chain2 ); | ^ In function ‘sprintf’, inlined from ‘calltmalign.isra’ at pairash.c:349:3: /usr/include/x86_64-linux-gnu/bits/stdio2.h:30:10: note: ‘__builtin___sprintf_chk’ output 3 or more bytes (assuming 10002) into a destination of size 10000 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c addsingle.c gcc -o maffttext2hex maffttext2hex.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread maffttext2hex.c: In function ‘main’: maffttext2hex.c:55:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 55 | fgets( (char *)buf, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -o hex2maffttext hex2maffttext.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c splittbfast.c splittbfast.c: In function ‘main’: splittbfast.c:3236:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3236 | system( com ); | ^~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c disttbfast.c disttbfast.c: In function ‘disttbfast’: disttbfast.c:4387:41: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 4387 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c tbfast.c tbfast.c: In function ‘main’: tbfast.c:3260:33: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 3260 | system( "cp infile.tree GuideTree" ); // tekitou | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c nodepair.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mafft-profile.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c f2cl.c f2cl.c: In function ‘main’: f2cl.c:297:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 297 | fgets( gett, B-1, orderfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c mccaskillwrap.c mccaskillwrap.c: In function ‘main’: mccaskillwrap.c:372:25: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 372 | system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mccaskillwrap.c: In function ‘athread’: mccaskillwrap.c:115:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 115 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:117:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c:129:17: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 129 | system( com ); // for cygwin, wakaran | ^~~~~~~~~~~~~ mccaskillwrap.c:155:25: warning: ignoring return value of ‘system’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | system( com ); | ^~~~~~~~~~~~~ mccaskillwrap.c: In function ‘readrawmccaskill’: mccaskillwrap.c:46:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 46 | fgets( gett, 999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c contrafoldwrap.c contrafoldwrap.c: In function ‘readcontrafold’: contrafoldwrap.c:57:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fgets( gett, 9999, fp ); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c countlen.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c seq2regtable.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c regtable2seq.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c score.c regtable2seq.c: In function ‘readereg’: regtable2seq.c:69:9: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c:97:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ regtable2seq.c: In function ‘readreg’: regtable2seq.c:120:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fgets( gett, 999, regfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c getlag.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c dndpre.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c setcore.c gcc -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o filter.o filter.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c replaceu.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c restoreu.c gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c setdirection.c restoreu.c: In function ‘main’: restoreu.c:185:25: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 185 | fgets( gett, 999, dlfp ); | ^~~~~~~~~~~~~~~~~~~~~~~~ setdirection.c: In function ‘main’: setdirection.c:132:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 132 | fgets( line, 99, difp ); | ^~~~~~~~~~~~~~~~~~~~~~~ gcc -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c makedirectionlist.c gcc -o version version.c -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread sed "s:_LIBDIR:/usr/lib/mafft/lib/mafft:" mafft.tmpl > mafft sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-homologs.tmpl > mafft-homologs.rb sed "s:_BINDIR:/usr/lib/mafft/bin:" mafft-sparsecore.tmpl > mafft-sparsecore.rb gcc -o dvtditr mtxutl.o io.o mltaln9.o tddis.o constants.o nj.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o MSalignmm.o fftFunctions.o fft.o tditeration.o dvtditr.o defs.o SAalignmm.o treeOperation.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndfast7 dndfast7.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndblast dndblast.o io.o constants.o mtxutl.o mltaln9.o tddis.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o sextet5 io.o constants.o mtxutl.o mltaln9.o tddis.o sextet5.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-distance io.o constants.o mtxutl.o mltaln9.o tddis.o mafft-distance.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairlocalalign mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairlocalalignmain.o pairlocalalign.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o multi2hat3s mtxutl.o io.o mltaln9.o tddis.o constants.o multi2hat3s.o defs.o fft.o fftFunctions.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o pairash mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o MSalignmm.o Galign11.o Lalign11.o genalign11.o MSalign11.o suboptalign11.o SAalignmm.o pairash.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o addsingle mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o addsingle.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o splittbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o splittbfast.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o disttbfast mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o disttbfast.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o tbfast mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o tbfast.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o nodepair mtxutl.o io.o mltaln9.o tddis.o constants.o MSalignmm.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o nodepair.o defs.o fft.o fftFunctions.o addfunctions.o pairlocalalign.o MSalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mafft-profile io.o mtxutl.o mltaln9.o tddis.o constants.o partSalignmm.o MSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o SAalignmm.o Galign11.o Lalign11.o genalign11.o Falign.o Falign_localhom.o fftFunctions.o fft.o mafft-profile.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o f2cl mtxutl.o io.o f2cl.o constants.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o mccaskillwrap mtxutl.o io.o mccaskillwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o contrafoldwrap mtxutl.o io.o contrafoldwrap.o constants.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o countlen mtxutl.o io.o countlen.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o seq2regtable mtxutl.o io.o seq2regtable.o defs.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o regtable2seq mtxutl.o io.o regtable2seq.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o score io.o mtxutl.o mltaln9.o score.o constants.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o getlag mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o Dalignmm.o getlag.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o dndpre dndpre.o io.o constants.o mtxutl.o mltaln9.o defs.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setcore mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o setcore.o defs.o fft.o fftFunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o filter mtxutl.o io.o filter.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o replaceu mtxutl.o io.o replaceu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o restoreu mtxutl.o io.o restoreu.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o setdirection mtxutl.o io.o setdirection.o defs.o mltaln9.o Galign11.o Lalign11.o genalign11.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread gcc -o makedirectionlist mtxutl.o io.o mltaln9.o tddis.o constants.o partSalignmm.o Lalignmm.o rna.o Salignmm.o Dalignmm.o Falign.o Falign_localhom.o Galign11.o Lalign11.o genalign11.o SAalignmm.o MSalignmm.o makedirectionlist.o defs.o fft.o fftFunctions.o addfunctions.o -Denablemultithread -std=c99 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/mafft-QKGPm6/mafft-7.525=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -lm -lpthread cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* done. make[2]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525/core' make[1]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525' dh_auto_test -O--sourcedirectory=core create-stamp debian/debhelper-build-stamp dh_testroot -O--sourcedirectory=core dh_prep -O--sourcedirectory=core debian/rules override_dh_auto_install make[1]: Entering directory '/build/mafft-QKGPm6/mafft-7.525' dh_auto_install -- PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft cd core && make -j2 install DESTDIR=/build/mafft-QKGPm6/mafft-7.525/debian/mafft AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" PREFIX=/usr/lib/mafft MANDIR=/usr/share/man/man1 LIBDIR=/usr/lib/mafft/lib/mafft make[2]: Entering directory '/build/mafft-QKGPm6/mafft-7.525/core' cp mafft mafft-homologs.rb mafft-sparsecore.rb ../scripts chmod 755 ../scripts/* cp mafftash_premafft.pl seekquencer_premafft.pl dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ../binaries chmod 755 ../binaries/* done. mkdir -p /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/lib/mafft chmod 755 /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/lib/mafft mkdir -p /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/bin chmod 755 /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/bin chmod 755 mafft mafft-homologs.rb mafft-sparsecore.rb install --strip-program=true mafft mafft-homologs.rb mafft-sparsecore.rb /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/bin install: WARNING: ignoring --strip-program option as -s option was not specified chmod 755 dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # in MinGW, it's ok if this fails strip dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version ||: # may fail for dash_client on mac. install --strip-program=true dvtditr dndfast7 dndblast sextet5 mafft-distance pairlocalalign multi2hat3s pairash addsingle maffttext2hex hex2maffttext splittbfast disttbfast tbfast nodepair mafft-profile f2cl mccaskillwrap contrafoldwrap countlen seq2regtable regtable2seq score getlag dndpre setcore filter replaceu restoreu setdirection makedirectionlist version /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified install --strip-program=true mafftash_premafft.pl seekquencer_premafft.pl /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/lib/mafft install: WARNING: ignoring --strip-program option as -s option was not specified ( cd /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/lib/mafft/bin; \ rm -f linsi ginsi einsi fftns fftnsi nwns nwnsi xinsi qinsi; \ rm -f mafft-linsi mafft-ginsi mafft-einsi mafft-fftns mafft-fftnsi mafft-nwns mafft-nwnsi mafft-xinsi mafft-qinsi mafft-randomcore.rb ; \ ln -s mafft linsi; ln -s mafft ginsi; ln -s mafft fftns; \ ln -s mafft fftnsi; ln -s mafft nwns; ln -s mafft nwnsi; \ ln -s mafft einsi; \ ln -s mafft mafft-linsi; ln -s mafft mafft-ginsi; ln -s mafft mafft-fftns; \ ln -s mafft mafft-fftnsi; ln -s mafft mafft-nwns; ln -s mafft mafft-nwnsi; \ ln -s mafft mafft-einsi; ln -s mafft mafft-xinsi; ln -s mafft mafft-qinsi;\ rm -f mafft-profile mafft-profile.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-profile .; \ rm -f mafft-distance mafft-distance.exe; ln -s /usr/lib/mafft/lib/mafft/mafft-distance . ) mkdir -p /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/share/man/man1 chmod 755 /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/share/man/man1 install --strip-program=true -m 644 mafft.1 mafft-homologs.1 /build/mafft-QKGPm6/mafft-7.525/debian/mafft/usr/share/man/man1 install: WARNING: ignoring --strip-program option as -s option was not specified make[2]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525/core' make[1]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525' dh_installdocs -O--sourcedirectory=core dh_installchangelogs -O--sourcedirectory=core dh_installman -O--sourcedirectory=core dh_installsystemduser -O--sourcedirectory=core dh_perl -O--sourcedirectory=core dh_link -O--sourcedirectory=core dh_strip_nondeterminism -O--sourcedirectory=core debian/rules override_dh_compress make[1]: Entering directory '/build/mafft-QKGPm6/mafft-7.525' dh_compress -X test/sample make[1]: Leaving directory '/build/mafft-QKGPm6/mafft-7.525' dh_fixperms -O--sourcedirectory=core dh_missing -O--sourcedirectory=core dh_dwz -a -O--sourcedirectory=core dwz: debian/mafft/usr/lib/mafft/lib/mafft/addsingle: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/contrafoldwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/countlen: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/disttbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndblast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndfast7: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dndpre: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/dvtditr: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/f2cl: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/filter: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/getlag: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/hex2maffttext: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-distance: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mafft-profile: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/maffttext2hex: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/makedirectionlist: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/mccaskillwrap: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/multi2hat3s: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/nodepair: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairash: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/pairlocalalign: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/regtable2seq: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/replaceu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/restoreu: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/score: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/seq2regtable: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setcore: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/setdirection: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/sextet5: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/splittbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/tbfast: .debug_info section not present dwz: debian/mafft/usr/lib/mafft/lib/mafft/version: .debug_info section not present dwz: Too few files for multifile optimization dh_dwz: warning: No dwz multifile created, but not explicitly requested either so ignoring it. dh_dwz: warning: Common issues include no debug information at all (missing -g) and dh_dwz: warning: compressed debug information (#931891). dh_strip -a -O--sourcedirectory=core dh_makeshlibs -a -O--sourcedirectory=core dh_shlibdeps -a -O--sourcedirectory=core dh_installdeb -O--sourcedirectory=core dh_gencontrol -O--sourcedirectory=core dh_md5sums -O--sourcedirectory=core dh_builddeb -O--sourcedirectory=core dpkg-deb: building package 'mafft' in '../mafft_7.525-1_amd64.deb'. dpkg-genbuildinfo -O../mafft_7.525-1_amd64.buildinfo dpkg-genchanges -O../mafft_7.525-1_amd64.changes dpkg-genchanges: info: including full source code in upload dpkg-source -Zxz --after-build . dpkg-buildpackage: info: full upload (original source is included) -------------------------------------------------------------------------------- Build finished at 2025-09-05T16:02:20Z Finished -------- I: Built successfully +------------------------------------------------------------------------------+ | Changes Fri, 05 Sep 2025 16:02:20 +0000 | +------------------------------------------------------------------------------+ mafft_7.525-1_amd64.changes: ---------------------------- Format: 1.8 Date: Fri, 05 Sep 2025 11:12:08 +0200 Source: mafft Binary: mafft Architecture: source amd64 Version: 7.525-1 Distribution: perl-5.42-throwaway Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Michael R. Crusoe Description: mafft - Multiple alignment program for amino acid or nucleotide sequences Closes: 1097352 Changes: mafft (7.525-1) unstable; urgency=medium . * Team upload. * New upstream version * Standards-Version: 4.7.2 (routine-update) * Added patch to support GCC 15. Closes: #1097352 * d/rules: no longer need to remove extra manual pages. * d/control: recommend ncbi-blast+ instead of blast2 Checksums-Sha1: f5f23c95e45c0ea10088a07318fdc5da21bf105b 1061 mafft_7.525-1.dsc a87733c60bb169d1945d0b040891acbc6562724a 622798 mafft_7.525.orig.tar.gz 5689597d19d230fc9b5bc85d49d28ddb100310e8 8180 mafft_7.525-1.debian.tar.xz 07cb5247ad676662d649722f477f12c667585239 4944 mafft_7.525-1_amd64.buildinfo db7bdb52f06571fe8b03278c5df317188ce026a9 1193768 mafft_7.525-1_amd64.deb Checksums-Sha256: d6af5a2842671b948ed5171e77d8730ead72930c6bfa43131b31c6979730eb5b 1061 mafft_7.525-1.dsc edb34ae9b26d6b55328c18fa060ed741bca8cd599c2f4f8fad0e0871c8082265 622798 mafft_7.525.orig.tar.gz 4a5812414bd4fa4c703e75fa6224b0f9a7c02a4dc7affec13a59bf794893f6b7 8180 mafft_7.525-1.debian.tar.xz aeee196c12d16ab6f5bd122171002d6b4061ec89b7e0c766c1431e226b0cb6b7 4944 mafft_7.525-1_amd64.buildinfo 6a885039a7d0c82f751069a182326b9dbd1a1b8e42c994497fb93da391dc40af 1193768 mafft_7.525-1_amd64.deb Files: 8d331fca1f2254d4e4dad297affe434e 1061 science optional mafft_7.525-1.dsc 0692b3874b73f8b93be204fcfc542254 622798 science optional mafft_7.525.orig.tar.gz 3397c0f9ca927006ed1689c2fe34dc94 8180 science optional mafft_7.525-1.debian.tar.xz c7b184d03a26cdce5cbb2555070867c5 4944 science optional mafft_7.525-1_amd64.buildinfo 7dc570cacd3de2ee06653cca26eb02fd 1193768 science optional mafft_7.525-1_amd64.deb +------------------------------------------------------------------------------+ | Buildinfo Fri, 05 Sep 2025 16:02:20 +0000 | +------------------------------------------------------------------------------+ Format: 1.0 Source: mafft Binary: mafft Architecture: amd64 source Version: 7.525-1 Checksums-Md5: 8d331fca1f2254d4e4dad297affe434e 1061 mafft_7.525-1.dsc 7dc570cacd3de2ee06653cca26eb02fd 1193768 mafft_7.525-1_amd64.deb Checksums-Sha1: f5f23c95e45c0ea10088a07318fdc5da21bf105b 1061 mafft_7.525-1.dsc db7bdb52f06571fe8b03278c5df317188ce026a9 1193768 mafft_7.525-1_amd64.deb Checksums-Sha256: d6af5a2842671b948ed5171e77d8730ead72930c6bfa43131b31c6979730eb5b 1061 mafft_7.525-1.dsc 6a885039a7d0c82f751069a182326b9dbd1a1b8e42c994497fb93da391dc40af 1193768 mafft_7.525-1_amd64.deb Build-Origin: Debian Build-Architecture: amd64 Build-Date: Fri, 05 Sep 2025 16:02:20 +0000 Build-Path: /build/mafft-QKGPm6/mafft-7.525 Build-Tainted-By: usr-local-has-programs Installed-Build-Depends: autoconf (= 2.72-3.1), automake (= 1:1.17-4), autopoint (= 0.23.1-2), autotools-dev (= 20240727.1), base-files (= 14), base-passwd (= 3.6.7), bash (= 5.3-1), binutils (= 2.45-6), binutils-common (= 2.45-6), binutils-x86-64-linux-gnu (= 2.45-6), bsdextrautils (= 2.41.1-2), bsdutils (= 1:2.41.1-2), build-essential (= 12.12), bzip2 (= 1.0.8-6), coreutils (= 9.7-3), cpp (= 4:15.2.0-1), cpp-14 (= 14.3.0-6), cpp-14-x86-64-linux-gnu (= 14.3.0-6), cpp-15 (= 15.2.0-3), cpp-15-x86-64-linux-gnu (= 15.2.0-3), cpp-x86-64-linux-gnu (= 4:15.2.0-1), dash (= 0.5.12-12), debconf (= 1.5.91), debhelper (= 13.26), debianutils (= 5.23.2), dh-autoreconf (= 20), dh-strip-nondeterminism (= 1.14.2-1), diffutils (= 1:3.10-4), dpkg (= 1.22.21), dpkg-dev (= 1.22.21), dwz (= 0.16-2), file (= 1:5.46-5), findutils (= 4.10.0-3), g++ (= 4:15.2.0-1), g++-15 (= 15.2.0-3), g++-15-x86-64-linux-gnu (= 15.2.0-3), g++-x86-64-linux-gnu (= 4:15.2.0-1), gcc (= 4:15.2.0-1), gcc-14 (= 14.3.0-6), gcc-14-base (= 14.3.0-6), gcc-14-x86-64-linux-gnu (= 14.3.0-6), gcc-15 (= 15.2.0-3), gcc-15-base (= 15.2.0-3), gcc-15-x86-64-linux-gnu (= 15.2.0-3), gcc-x86-64-linux-gnu (= 4:15.2.0-1), gettext (= 0.23.1-2+b1), gettext-base (= 0.23.1-2+b1), grep (= 3.11-4), groff-base (= 1.23.0-9), gzip (= 1.13-1), hostname (= 3.25), init-system-helpers (= 1.69), intltool-debian (= 0.35.0+20060710.6), libacl1 (= 2.3.2-2+b1), libarchive-zip-perl (= 1.68-1), libasan8 (= 15.2.0-3), libatomic1 (= 15.2.0-3), libattr1 (= 1:2.5.2-3), libaudit-common (= 1:4.0.5-1), libaudit1 (= 1:4.0.5-1), libbinutils (= 2.45-6), libblkid1 (= 2.41.1-2), libbz2-1.0 (= 1.0.8-6), libc-bin (= 2.41-12), libc-dev-bin (= 2.41-12), libc6 (= 2.41-12), libc6-dev (= 2.41-12), libcap-ng0 (= 0.8.5-4+b1), libcap2 (= 1:2.75-10+b1), libcc1-0 (= 15.2.0-3), libcrypt-dev (= 1:4.4.38-1), libcrypt1 (= 1:4.4.38-1), libctf-nobfd0 (= 2.45-6), libctf0 (= 2.45-6), libdb5.3t64 (= 5.3.28+dfsg2-9), libdebconfclient0 (= 0.280), libdebhelper-perl (= 13.26), libdpkg-perl (= 1.22.21), libelf1t64 (= 0.193-2), libfile-stripnondeterminism-perl (= 1.14.2-1), libgcc-14-dev (= 14.3.0-6), libgcc-15-dev (= 15.2.0-3), libgcc-s1 (= 15.2.0-3), libgdbm-compat4t64 (= 1.26-1), libgdbm6t64 (= 1.26-1), libgmp10 (= 2:6.3.0+dfsg-5), libgomp1 (= 15.2.0-3), libgprofng0 (= 2.45-6), libhwasan0 (= 15.2.0-3), libisl23 (= 0.27-1), libitm1 (= 15.2.0-3), libjansson4 (= 2.14-2+b3), liblastlog2-2 (= 2.41.1-2), liblsan0 (= 15.2.0-3), liblzma5 (= 5.8.1-1.1), libmagic-mgc (= 1:5.46-5), libmagic1t64 (= 1:5.46-5), libmd0 (= 1.1.0-2+b1), libmount1 (= 2.41.1-2), libmpc3 (= 1.3.1-2), libmpfr6 (= 4.2.2-2), libpam-modules (= 1.7.0-5), libpam-modules-bin (= 1.7.0-5), libpam-runtime (= 1.7.0-5), libpam0g (= 1.7.0-5), libpcre2-8-0 (= 10.46-1), libperl5.42 (= 5.42.0-2), libpipeline1 (= 1.5.8-1), libquadmath0 (= 15.2.0-3), libseccomp2 (= 2.6.0-2), libselinux1 (= 3.8.1-1), libsframe2 (= 2.45-6), libsmartcols1 (= 2.41.1-2), libsqlite3-0 (= 3.46.1-7), libssl3t64 (= 3.5.2-1), libstdc++-15-dev (= 15.2.0-3), libstdc++6 (= 15.2.0-3), libsystemd0 (= 258~rc4-1), libtinfo6 (= 6.5+20250216-2), libtool (= 2.5.4-5), libtsan2 (= 15.2.0-3), libubsan1 (= 15.2.0-3), libuchardet0 (= 0.0.8-2), libudev1 (= 258~rc4-1), libunistring5 (= 1.3-2), libuuid1 (= 2.41.1-2), libxml2-16 (= 2.14.5+dfsg-0.2), libzstd1 (= 1.5.7+dfsg-1.1), linux-libc-dev (= 6.16.3-1), m4 (= 1.4.20-1), make (= 4.4.1-2), man-db (= 2.13.1-1), mawk (= 1.3.4.20250131-1), ncurses-base (= 6.5+20250216-2), ncurses-bin (= 6.5+20250216-2), openssl-provider-legacy (= 3.5.2-1), patch (= 2.8-2), perl (= 5.42.0-2), perl-base (= 5.42.0-2), perl-modules-5.42 (= 5.42.0-2), po-debconf (= 1.0.21+nmu1), rpcsvc-proto (= 1.4.3-1), sed (= 4.9-2), sensible-utils (= 0.0.26), sysvinit-utils (= 3.14-4), tar (= 1.35+dfsg-3.1), util-linux (= 2.41.1-2), xz-utils (= 5.8.1-1.1), zlib1g (= 1:1.3.dfsg+really1.3.1-1+b1) Environment: DEB_BUILD_OPTIONS="parallel=2" LANG="C.UTF-8" LC_COLLATE="C.UTF-8" LC_CTYPE="C.UTF-8" LD_LIBRARY_PATH="/usr/lib/libeatmydata" SOURCE_DATE_EPOCH="1757063528" +------------------------------------------------------------------------------+ | Package contents Fri, 05 Sep 2025 16:02:20 +0000 | +------------------------------------------------------------------------------+ mafft_7.525-1_amd64.deb ----------------------- new Debian package, version 2.0. size 1193768 bytes: control archive=2392 bytes. 1392 bytes, 30 lines control 3912 bytes, 56 lines md5sums Package: mafft Version: 7.525-1 Architecture: amd64 Maintainer: Debian Med Packaging Team Installed-Size: 13669 Depends: libc6 (>= 2.34), perl:any Recommends: ncbi-blast+, libwww-perl, lynx, ruby Enhances: t-coffee Section: science Priority: optional Homepage: https://mafft.cbrc.jp/alignment/software/ Description: Multiple alignment program for amino acid or nucleotide sequences MAFFT is a multiple sequence alignment program which offers three accuracy-oriented methods: * L-INS-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information), * G-INS-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information), * E-INS-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences), and five speed-oriented methods: * FFT-NS-i (iterative refinement method; two cycles only), * FFT-NS-i (iterative refinement method; max. 1000 iterations), * FFT-NS-2 (fast; progressive method), * FFT-NS-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree), * NW-NS-PartTree-1 (recommended for ∼50,000 sequences; progressive method with the PartTree algorithm). drwxr-xr-x root/root 0 2025-09-05 09:12 ./ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/bin/ lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/bin/mafft -> ../lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/bin/mafft-homologs -> ../lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/bin/mafft-profile -> ../lib/mafft/bin/mafft-profile drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/lib/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/lib/mafft/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/ lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/einsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/fftns -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/fftnsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/ginsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/linsi -> mafft -rwxr-xr-x root/root 109789 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-distance -> ../lib/mafft/mafft-distance lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-einsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-fftns -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-fftnsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-ginsi -> mafft -rwxr-xr-x root/root 11551 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-homologs.rb lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-linsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-nwns -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-nwnsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-profile -> ../lib/mafft/mafft-profile lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-qinsi -> mafft -rwxr-xr-x root/root 7788 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-sparsecore.rb lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/mafft-xinsi -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/nwns -> mafft lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/lib/mafft/bin/nwnsi -> mafft drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/lib/mafft/lib/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/ -rwxr-xr-x root/root 686224 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/addsingle -rwxr-xr-x root/root 366736 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/contrafoldwrap -rwxr-xr-x root/root 116992 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/countlen -rwxr-xr-x root/root 710800 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/disttbfast -rwxr-xr-x root/root 387216 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/dndblast -rwxr-xr-x root/root 387216 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/dndfast7 -rwxr-xr-x root/root 366736 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/dndpre -rwxr-xr-x root/root 706704 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/dvtditr -rwxr-xr-x root/root 178400 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/f2cl -rwxr-xr-x root/root 305408 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/filter -rwxr-xr-x root/root 628880 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/getlag -rwxr-xr-x root/root 14352 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/hex2maffttext -rwxr-xr-x root/root 387216 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/mafft-distance -rwxr-xr-x root/root 628880 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/mafft-profile -rwxr-xr-x root/root 10475 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/mafftash_premafft.pl -rwxr-xr-x root/root 14352 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/maffttext2hex -rwxr-xr-x root/root 657568 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/makedirectionlist -rwxr-xr-x root/root 366736 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/mccaskillwrap -rwxr-xr-x root/root 395408 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/multi2hat3s -rwxr-xr-x root/root 694416 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/nodepair -rwxr-xr-x root/root 641168 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/pairash -rwxr-xr-x root/root 665744 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/pairlocalalign -rwxr-xr-x root/root 305408 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/regtable2seq -rwxr-xr-x root/root 305408 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/replaceu -rwxr-xr-x root/root 305408 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/restoreu -rwxr-xr-x root/root 362640 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/score -rwxr-xr-x root/root 15541 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/seekquencer_premafft.pl -rwxr-xr-x root/root 116992 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/seq2regtable -rwxr-xr-x root/root 628880 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/setcore -rwxr-xr-x root/root 305416 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/setdirection -rwxr-xr-x root/root 387216 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/sextet5 -rwxr-xr-x root/root 653456 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/splittbfast -rwxr-xr-x root/root 743568 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/tbfast -rwxr-xr-x root/root 14352 2025-09-05 09:12 ./usr/lib/mafft/lib/mafft/version drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/doc/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/doc/mafft/ -rw-r--r-- root/root 995 2025-09-05 09:12 ./usr/share/doc/mafft/changelog.Debian.gz -rw-r--r-- root/root 2013 2025-09-05 08:59 ./usr/share/doc/mafft/copyright drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/doc/mafft/test/ -rw-r--r-- root/root 16616 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample -rw-r--r-- root/root 30112 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.dpparttree -rw-r--r-- root/root 28816 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.fftns2 -rw-r--r-- root/root 28996 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.fftnsi -rw-r--r-- root/root 29896 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.gins1 -rw-r--r-- root/root 29572 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.ginsi -rw-r--r-- root/root 41380 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.ginsi.allowshift -rw-r--r-- root/root 28888 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.lins1 -rw-r--r-- root/root 29500 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.linsi -rw-r--r-- root/root 30112 2024-03-17 01:36 ./usr/share/doc/mafft/test/sample.parttree -rw-r--r-- root/root 1502 2024-03-17 01:36 ./usr/share/doc/mafft/test/samplerna -rw-r--r-- root/root 1916 2024-03-17 01:36 ./usr/share/doc/mafft/test/samplerna.qinsi -rw-r--r-- root/root 1916 2024-03-17 01:36 ./usr/share/doc/mafft/test/samplerna.xinsi -rw-r--r-- root/root 908 2024-03-17 01:36 ./usr/share/doc/mafft/test/script -rw-r--r-- root/root 7292 2024-03-17 01:36 ./usr/share/doc/mafft/test/x.gz drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/man/ drwxr-xr-x root/root 0 2025-09-05 09:12 ./usr/share/man/man1/ lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/ginsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-einsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-fftns.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-fftnsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-ginsi.1.gz -> mafft.1.gz -rw-r--r-- root/root 2130 2025-09-05 09:12 ./usr/share/man/man1/mafft-homologs.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-linsi.1.gz -> mafft.1.gz lrwxrwxrwx root/root 0 2025-09-05 09:12 ./usr/share/man/man1/mafft-profile.1.gz -> mafft.1.gz -rw-r--r-- root/root 4421 2025-09-05 09:12 ./usr/share/man/man1/mafft.1.gz +------------------------------------------------------------------------------+ | Post Build Fri, 05 Sep 2025 16:02:20 +0000 | +------------------------------------------------------------------------------+ +------------------------------------------------------------------------------+ | Cleanup Fri, 05 Sep 2025 16:02:20 +0000 | +------------------------------------------------------------------------------+ Purging /build/mafft-QKGPm6 Not cleaning session: cloned chroot in use +------------------------------------------------------------------------------+ | Summary Fri, 05 Sep 2025 16:02:21 +0000 | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: full Build-Space: 83828 Build-Time: 37 Distribution: perl-5.42-throwaway Host Architecture: amd64 Install-Time: 4 Job: /srv/debomatic/incoming/mafft_7.525-1.dsc Machine Architecture: amd64 Package: mafft Package-Time: 45 Source-Version: 7.525-1 Space: 83828 Status: successful Version: 7.525-1 -------------------------------------------------------------------------------- Finished at 2025-09-05T16:02:20Z Build needed 00:00:45, 83828k disk space